Translate: Add short RK name.

.gitlab-ci.yml

@@ -1,5 +1,5 @@
 # .gitlab-ci.yml -- Pamhyr gitlab-ci
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -20,6 +20,8 @@ stages:
   - test
   - build
   - package
+  - hash
+  - antivirus
   - release
 
 #############
@@ -27,9 +29,9 @@ stages:
 #############
 
 variables:
-  MAGE_VERSION: "v8.3.3"
+  MAGE_8_VERSION: "v8.3.6"
 
-dl-mage-doc:
+dl-mage8-doc:
   stage: downloads
   tags:
     - linux
@@ -38,46 +40,48 @@ dl-mage-doc:
   script:
     - mkdir -p doc
     - cd doc
-    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_VERSION/downloads/documents/Mage-8_Documentation.pdf
+    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/documents/Mage-8_Documentation.pdf
   artifacts:
     paths:
       - doc/mage8.pdf
 
-dl-mage-linux:
+dl-mage8-linux:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_VERSION/downloads/packages/mage_linux.tgz
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_linux.tgz
-    - mkdir -p mage-linux
+    - mkdir -p mage8-linux
-    - cd mage-linux
+    - cd mage8-linux
-    - tar xvf ../mage.tgz
+    - tar xvf ../mage8.tgz
   artifacts:
     paths:
-      - mage-linux/mage
+      - mage8-linux/mage
-      - mage-linux/mage_extraire
+      - mage8-linux/mage_as7
-      - mage-linux/mailleurTT
+      - mage8-linux/mage_extraire
-      - mage-linux/libbief.so
+      - mage8-linux/mailleurTT
+      - mage8-linux/libbief.so
 
-dl-mage-windows:
+dl-mage8-windows:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_VERSION/downloads/packages/mage_windows.tgz
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_windows.tgz
-    - mkdir -p mage-windows
+    - mkdir -p mage8-windows
-    - cd mage-windows
+    - cd mage8-windows
-    - tar xvf ../mage.tgz
+    - tar xvf ../mage8.tgz
   artifacts:
     paths:
-      - mage-windows/mage.exe
+      - mage8-windows/mage.exe
-      - mage-windows/mage_extraire.exe
+      - mage8-windows/mage_as7.exe
-      - mage-windows/mailleurTT.exe
+      - mage8-windows/mage_extraire.exe
-      - mage-windows/libbief.dll
+      - mage8-windows/mailleurTT.exe
+      - mage8-windows/libbief.dll
 
 #############
 # CONFIGURE #
@@ -148,23 +152,22 @@ test-pep8:
 # BUILD #
 #########
 
-build-users-doc:
+# build-users-doc:
-  stage: build
+#   stage: build
-  tags:
+#   tags:
-    - linux
+#     - linux
-  needs:
+#   needs:
-    - job: set-version
+#     - job: set-version
-      artifacts: true
+#       artifacts: true
-  script:
+#   script:
-    - cd ./doc/users/
+#     - cd ./doc/users/
-    - ./build.sh
+#     - ./build.sh
-  artifacts:
+#   artifacts:
-    paths:
+#     paths:
-      - doc/users/documentation.pdf
+#       - doc/users/documentation.pdf
-      - doc/users/documentation.html
+#       - doc/users/documentation.html
-      - doc/users/images/
+#       - doc/users/images/
-  allow_failure: true
+#   allow_failure: true
-
 
 build-td:
   stage: build
@@ -221,9 +224,9 @@ build-linux:
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   needs:
-    - job: dl-mage-linux
+    - job: dl-mage8-linux
       artifacts: true
-    - job: dl-mage-doc
+    - job: dl-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -231,8 +234,8 @@ build-linux:
       artifacts: true
     - job: build-developers-doc
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
-      artifacts: true
+    #   artifacts: true
     - job: build-td
       artifacts: true
   script:
@@ -248,28 +251,32 @@ build-linux:
     - pyinstaller -y --paths linux-venv/lib/python3.8/site-packages ../src/pamhyr.py
     # Create directory
     - mkdir -p pamhyr
-    - mkdir -p pamhyr/pamhyr
+    - mkdir -p pamhyr/_internal
-    - mkdir -p pamhyr/pamhyr/_internal
     # Copy Pamhyr info
-    - cp -v ../VERSION pamhyr/pamhyr/_internal/
+    - cp -v ../VERSION pamhyr/_internal/
-    - cp -v ../AUTHORS pamhyr/pamhyr/_internal/
+    - cp -v ../AUTHORS pamhyr/_internal/
-    - cp -v ../LICENSE pamhyr/pamhyr/_internal/
+    - cp -v ../LICENSE pamhyr/_internal/
-    - cp -v ../src/motd.txt pamhyr/pamhyr/_internal/
+    - cp -v ../src/motd.txt pamhyr/_internal/
     # Copy mage
-    - mkdir -p pamhyr/mage
+    - mkdir -p pamhyr/mage8
-    - cp -v ../mage-linux/* pamhyr/mage/
+    - cp -v ../mage8-linux/* pamhyr/mage8/
     # Copy Pamhyr
-    - cp -r dist/pamhyr pamhyr/
+    - cp -r dist/pamhyr/* pamhyr/
+    # Pamhyr script to force x11
+    - echo '#!/usr/bin/env bash' > pamhyr/pamhyr-x11
+    - echo "" >> pamhyr/pamhyr-x11
+    - echo "GDK_BACKEND=x11 ./pamhyr $@" >> pamhyr/pamhyr-x11
+    - chmod +x pamhyr/pamhyr-x11
     # Copy Pamhyr resources
-    - mkdir -p pamhyr/pamhyr/_internal/View
+    - mkdir -p pamhyr/_internal/View
-    - mkdir -p pamhyr/pamhyr/_internal/View/ui
+    - mkdir -p pamhyr/_internal/View/ui
-    - mkdir -p pamhyr/pamhyr/_internal/View/ui/Widgets
+    - mkdir -p pamhyr/_internal/View/ui/Widgets
-    - cp -r ../src/View/ui/*.ui pamhyr/pamhyr/_internal/View/ui/
+    - cp -r ../src/View/ui/*.ui pamhyr/_internal/View/ui/
-    - cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/_internal/View/ui
+    - cp -r ../src/View/ui/ressources/ pamhyr/_internal/View/ui
-    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/_internal/View/ui/Widgets
+    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/_internal/View/ui/Widgets
     # Copy lang
-    - mkdir -p pamhyr/pamhyr/_internal/lang
+    - mkdir -p pamhyr/_internal/lang
-    - cp -r ../src/lang/*.qm pamhyr/pamhyr/_internal/lang
+    - cp -r ../src/lang/*.qm pamhyr/_internal/lang
     # Copy tests cases
     - mkdir -p pamhyr/tests_cases/
     - mkdir -p pamhyr/tests_cases/Saar
@@ -297,10 +304,6 @@ build-linux:
     # Copy TP charriage
     - mkdir -p pamhyr/doc/TP_charriage/
     - cp ../doc/users/TP_charriage/* pamhyr/doc/TP_charriage
-    # Create running script
-    - echo "#!/bin/sh" > pamhyr/Pamhyr2
-    - echo "./pamhyr/pamhyr $@" >> pamhyr/Pamhyr2
-    - chmod u+x pamhyr/Pamhyr2
   artifacts:
     paths:
       - linux/pamhyr
@@ -312,9 +315,9 @@ build-windows:
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   needs:
-    - job: dl-mage-windows
+    - job: dl-mage8-windows
       artifacts: true
-    - job: dl-mage-doc
+    - job: dl-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -322,18 +325,20 @@ build-windows:
       artifacts: true
     - job: build-developers-doc
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
-      artifacts: true
+    #   artifacts: true
     - job: build-td
       artifacts: true
   script:
     - mkdir windows
     - cd windows
     # Setup env
+    - python -m pip install -U pip
     - python -m pip install -r ..\requirements.txt
     - python -m pip install -U -r ..\requirements.txt
     # Run Pyinstaller
-    - pyinstaller -y ..\src\pamhyr.py
+    # - pyinstaller --noconsole -y ..\src\pamhyr.py
+    - pyinstaller -i ../src/View/ui/ressources/icon.ico --hide-console hide-early -y ..\src\pamhyr.py
     # Create directory
     - mkdir pamhyr
     - dir
@@ -403,6 +408,111 @@ windows-package-exe:
     - copy ..\packages\pamhyr.nsi pamhyr.nsi
     - .\make-windows-exe.bat
 
+########
+# HASH #
+########
+
+linux-build-hash:
+  stage: hash
+  tags:
+    - release
+    - linux
+  needs:
+    - job: build-linux
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - cd linux
+    - sha256sum -b pamhyr/pamhyr > pamhyr/pamhyr.sha256
+  artifacts:
+    paths:
+      - linux/pamhyr/pamhyr.sha256
+
+windows-build-hash:
+  stage: hash
+  tags:
+    - release
+    - linux
+  needs:
+    - job: build-windows
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - cd windows
+    - sha256sum -b pamhyr/pamhyr.exe > pamhyr/pamhyr.exe.sha256
+  artifacts:
+    paths:
+      - windows/pamhyr/pamhyr.exe.sha256
+
+pkg-hash:
+  stage: hash
+  tags:
+    - release
+    - linux
+  needs:
+    - job: linux-package-tar
+      artifacts: true
+    - job: windows-package-zip
+      artifacts: true
+    - job: windows-package-exe
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
+  script:
+    - cd windows
+    - sha256sum -b pamhyr-windows.exe > pamhyr-windows.exe.sha256
+    - sha256sum -b pamhyr-windows.zip > pamhyr-windows.zip.sha256
+    - cd ..
+    - cd linux
+    - sha256sum -b pamhyr-gnulinux.tar.xz > pamhyr-gnulinux.tar.xz.sha256
+  artifacts:
+    paths:
+    - windows/pamhyr-windows.exe.sha256
+    - windows/pamhyr-windows.zip.sha256
+    - linux/pamhyr-gnulinux.tar.xz.sha256
+
+#############
+# ANTIVIRUS #
+#############
+
+build-check-clamav:
+  stage: antivirus
+  tags:
+    - release
+    - linux
+  needs:
+    - job: build-linux
+      artifacts: true
+    - job: build-windows
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - cd packages
+    - ./clamav-scan.sh builds
+  allow_failure: true
+
+pkg-check-clamav:
+  stage: antivirus
+  tags:
+    - release
+    - linux
+  needs:
+    - job: linux-package-tar
+      artifacts: true
+    - job: windows-package-zip
+      artifacts: true
+    - job: windows-package-exe
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
+  script:
+    - cd packages
+    - ./clamav-scan.sh packages
+  allow_failure: true
+
 ###########
 # RELEASE #
 ###########
@@ -419,10 +529,12 @@ tag-release:
       artifacts: true
     - job: windows-package-exe
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
-      artifacts: true
+    #   artifacts: true
     - job: build-developers-doc
       artifacts: true
+    - job: pkg-hash
+      artifacts: true
   rules:
     - if: $CI_COMMIT_TAG
   artifacts:
@@ -430,33 +542,44 @@ tag-release:
       - linux/pamhyr-gnulinux.tar.xz
       - windows/pamhyr-windows.zip
       - windows/pamhyr-windows.exe
+      - linux/pamhyr-gnulinux.tar.xz.sha256
+      - windows/pamhyr-windows.zip.sha256
+      - windows/pamhyr-windows.exe.sha256
       - doc/dev/documentation.pdf
-      - doc/users/documentation.pdf
+      # - doc/users/documentation.pdf
   script:
     - cd packages
   release:
     name: '$CI_COMMIT_TAG'
-    description: 'Automatic release from tag $CI_COMMIT_TAG'
+    description: '$CI_COMMIT_TAG_MESSAGE'
     tag_name: '$CI_COMMIT_TAG'
     ref: '$CI_COMMIT_SHA'
     assets:
       links:
+        - name: 'GNU/Linux CHECKSUM SHA256 (tar.xz)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/linux/pamhyr-gnulinux.tar.xz.sha256'
+          filepath: '/linux/pamhyr-gnulinux.tar.xz.sha256'
+          link_type: 'package'
         - name: 'GNU/Linux (tar.xz)'
           url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/linux/pamhyr-gnulinux.tar.xz'
           filepath: '/linux/pamhyr-gnulinux.tar.xz'
           link_type: 'package'
+        - name: 'Windows CHECKSUM SHA256 (exe)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.exe.sha256'
+          filepath: '/windows/pamhyr-windows.exe.sha256'
+          link_type: 'package'
         - name: 'Windows (exe)'
           url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.exe'
           filepath: '/windows/pamhyr-windows.exe'
           link_type: 'package'
+        - name: 'Windows CHECKSUM SHA256 (zip)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.zip.sha256'
+          filepath: '/windows/pamhyr-windows.zip.sha256'
+          link_type: 'package'
         - name: 'Windows (zip)'
           url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.zip'
           filepath: '/windows/pamhyr-windows.zip'
           link_type: 'package'
-        - name: 'User documentations (pdf)'
-          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/doc/users/documentation.pdf'
-          filepath: '/doc/users/documentation.pdf'
-          link_type: 'other'
         - name: 'Dev documentations (pdf)'
           url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/doc/dev/documentation.pdf'
           filepath: '/doc/dev/documentation.pdf'

AUTHORS

@@ -1,3 +1,3 @@
 Sylvain COULIBALY, INRAE, 2020 - 2022
-Théophile TERRAZ, INRAE, 2022 - 2023
+Théophile TERRAZ, INRAE, 2022 - 2024
-Pierre-Antoine ROUBY, INRAE, 2023
+Pierre-Antoine ROUBY, INRAE, 2023 - 2024

README.md

@@ -25,21 +25,11 @@ for more details.
 
 ### GNU/Linux
 
-Downloads the [last
+[See documentation](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20GNULinux)
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
-GNU/Linux binary archive.
-
-```shell
-tar xf pamhyr-gnulinux.tar.xz
-cd pamhyr
-./Pamhyr2
-```
 
 ### Windows
 
-Downloads the [last
+[See documentation](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20Windows)
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
-Windows installer or ZIP archive.
 
 ### From source code
 

doc/dev/documentation.org

@@ -1,5 +1,5 @@
 # documentation.org -- Pamhyr developers documentation
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -369,6 +369,7 @@ of Bar (Listing [[sql-bar]] and [[sql-foo]]).
             CREATE TABLE bar (
               id INTEGER NOT NULL PRIMARY KEY,
               x INTEGER NOT NULL,
+              y INTEGER NOT NULL,
               foo_id INTEGER NOT NULL,
               FOREIGN KEY(foo_id) REFERENCES foo(id),
             )""")
@@ -455,6 +456,15 @@ of Bar (Listing [[sql-bar]] and [[sql-foo]]).
               bar._sql_save(execute, data=data)
 #+end_src
 
+Let see the results database scheme for Pamhyr2 at version v0.0.7 in
+Figure [[sql_schema]].
+
+#+NAME: sql_schema
+#+ATTR_LATEX: :width 16cm
+#+CAPTION: SQLite database scheme at Pamhyr2 version v0.0.7 (generate with [[https://gitlab.com/Screwtapello/sqlite-schema-diagram]])
+[[./images/schema_v0.0.7.png]]
+
+
 [fn:sqlite] The SQLite web site: https://www.sqlite.org/index.html
 (last access 2023-09-20)
 
@@ -538,44 +548,44 @@ generic value from optional parameters, for examples:
 #+NAME: window
 #+CAPTION: Example of Pamhyr2 window
 #+begin_src python :python python3 :results output :noweb yes
-    from View.Tools.PamhyrWindow import PamhyrWindow
+  from View.Tools.PamhyrWindow import PamhyrWindow
-    from View.My.Translate import MyTranslate
+  from View.My.Translate import MyTranslate
-    from View.My.Table import MyTableModel
+  from View.My.Table import MyTableModel
 
-    class MyWindow(PamhyrWindow):
+  class MyWindow(PamhyrWindow):
-        _pamhyr_ui = "MyUI"
+      _pamhyr_ui = "MyUI"
-        _pamhyr_name = "My window"
+      _pamhyr_name = "My window"
 
-        def __init__(self, my_data=None,
+      def __init__(self, study=None, config=None,
-                     study=None, config=None,
+                   my_data=None,
-                     parent=None):
+                   parent=None):
-            self._my_data = my_data
+          self._my_data = my_data
 
-            super(MyWindow, self).__init__(
+          super(MyWindow, self).__init__(
-                # Window title
+              # Window title
-                title = self._pamhyr_name + " - " + study.name,
+              title = self._pamhyr_name + " - " + study.name,
-                # Window standard data
+              # Window standard data
-                study = study, config = config,
+              study = study, config = config,
-                trad = MyTranslate(),
+              trad = MyTranslate(),
-                parent = parent,
+              parent = parent,
-                # Activate undo/redo and copy/paste shortcut
+              # Activate undo/redo and copy/paste shortcut
-                options = ["undo", "copy"]
+              options = ["undo", "copy"]
-            )
+          )
 
-            # Add custom data to hash window computation
+          # Add custom data to hash window computation
-            self._hash_data.append(self._my_data)
+          self._hash_data.append(self._my_data)
 
-            # Setup custom window components
+          # Setup custom window components
-            self.setup_table()
+          self.setup_table()
-            self.setup_connections()
+          self.setup_connections()
 
-        def setup_table(self):
+      def setup_table(self):
-            # Init table(s)...
+          # Init table(s)...
 
-        def setup_connections(self):
+      def setup_connections(self):
-            # Init action connection(s)...
+          # Init action connection(s)...
 
-        # ...
+      # ...
 #+end_src
 
 Typically we called method =setup_*=, the method to initialize some
@@ -636,7 +646,7 @@ class AddNodeCommand(QUndoCommand):
         self._node = node
 
     def undo(self):
-        self._graph.remove_node(self._node.name)
+        self._graph.remove_node(self._node)
 
     def redo(self):
         self._graph.insert_node(self._node)
@@ -661,11 +671,13 @@ creation, this stack is accessible at =self._undo_stack=.
 
 *** Plot
 
-To define a new plot you can create a class who inherit to APlot. The
+To define a new plot you can create a class who inherit to
-creator need threee argument:
+PamhyrPlot. The creator need at leaste five argument:
  - A =canvas= of type =MplCanvas=
+ - A (optional) =trad= of type =PamhyrTranslate=
  - A =data= used in =draw= and =update= to create and update the plot
  - A optional =toolbar= of type =PamhyrToolbar=
+ - A =parent= window
 This class must implement two method =draw= and =update=, the first
 method to draw the plot from scratch, the second to update the plot if
 data has changed.
@@ -673,19 +685,36 @@ data has changed.
 #+begin_src python :python python3 :results output :noweb yes
   from View.Tools.PamhyrPlot import PamhyrPlot
 
-  class MyPlot(APlot):
+  class MyPlot(PamhyrPlot):
-      def __init__(self, canvas=None, data=None, toolbar=None):
+      def __init__(self, canvas=None, trad=None, toolbar=None
+                   data=None, parent=None):
           super(MyPlot, self).__init__(
               canvas=canvas,
+              trad=trad,
               data=data,
-              toolbar=toolbar
+              toolbar=toolbar,
+              parent=parent
           )
 
+        self.label_x = self._trad["x"]
+        self.label_y = self._trad["y"]
+
+        # Optional configuration
+        self._isometric_axis = False
+
+        self._auto_relim_update = True
+        self._autoscale_update = True
+
       def draw(self):
           # Draw function code...
 
-      def update(self, ind = None):
+      def update(self):
           # Update function code...
+
+      def clear(self):
+          # Clear plot values...
+
+      # ...
 #+end_src
 
 ** Solver
@@ -745,7 +774,7 @@ execute a code on distant computer, for example, over ssh.
                   style=dashed;
                   subgraph cluster021 {
                       label="Solver Classes";
-                      classSolverM7[label="Mage7", fillcolor=6];
+                      //classSolverM7[label="Mage7", fillcolor=6];
                       classSolverM8[label="Mage8", fillcolor=6];
                       classSolverR[label="RubarBE", fillcolor=6];
                   }
@@ -828,7 +857,7 @@ solver and get results:
  - (2.1) The solver read the input file(s)
  - (2.2) The solver compute results and write it to solver output
    file(s)
- - (3) Pamhyr2 create a Reuslts
+ - (3) Pamhyr2 create a =Results= object
  - (3.1) The Pamhyr2 solver class read solver output file(s) and
    complete Results with readed data
 
@@ -958,8 +987,16 @@ different methods:
 
 ** Unit tests
 
-The unit tests is actually not implemented in Pamhyr2, it is a *work
+A very small part of Pamhyr2 has unit test. This part is limited to the Model.
-in progress*.
+
+#+begin_src shell
+  python3 -m venv test
+  . test test/bin/activate
+  pip3 install -U -r ./full-requirements.txt
+
+  cd src/
+  python3 -Walways -m unittest discovert -v -t .
+#+end_src
 
 ** The debug mode
 
@@ -970,14 +1007,14 @@ line:
 ./Pamhyr2 debug
 #+end_src
 
-This mode add some log and add two action in main window menu:
+This mode add some log and add two action in main window menu: "About
-"About/Debug" open a window with Python Repl in current Python
+> Debug" open a window with Python Repl in current Python
-environement, and "About/Debug SQLite" who open the application
+environement, and "About > Debug SQLite" who open the application
 SQLiteBrowser (if installed) on current Study to explore the study
 data base file.
 
 #+NAME: debug-repl
-#+ATTR_LATEX: :width 12cm
+#+ATTR_LATEX: :width 14cm
 #+CAPTION: Pamhyr2 debug Python REPL
 [[./images/python-debug-repl.png]]
 

doc/tools/PamhyrDoc.cls

@@ -11,7 +11,8 @@
 \usepackage[absolute]{textpos}
 \usepackage{titlesec}
 \usepackage{amssymb}
-\usepackage{tcolorbox}
+\usepackage[minted,xparse,breakable]{tcolorbox}
+\usepackage{pmboxdraw}
 
 \usepackage{enumitem}
 \setlist[enumerate]{itemsep=-0.5em}
@@ -140,7 +141,7 @@
 \setminted[llvm]{breaklines,fontsize=\footnotesize,encoding=utf8}
 
 %% Add box arrond of minted
-\BeforeBeginEnvironment{minted}{\begin{tcolorbox}[boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
+\BeforeBeginEnvironment{minted}{\begin{tcolorbox}[breakable, boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
 \AfterEndEnvironment{minted}{\end{tcolorbox}}%
 
 \makeatletter

full-requirements.txt

@@ -4,9 +4,11 @@ PyQt5-sip==12.12.2
 PyQtWebEngine==5.15.6
 QScintilla>=2.14.1
 pyqtgraph>=0.12.1
-matplotlib>=3.4.1
+matplotlib>=3.7.1
 numpy>=1.24.2
 colorama>=0.4.3
 pyinstaller>=5.11.0
 shapely>=2.0.1
 lxml>=4.9.3
+platformdirs>=4.2.0
+pyshp>=2.3.1

packages/clamav-scan.sh

@@ -0,0 +1,21 @@
+#! /bin/bash
+set +x
+
+OPTS="-r -a -i"
+
+if [ "$1" == "builds" ]; then
+    FILES="../windows/ ../linux/"
+else
+    FILES="../windows/pamhyr-windows.exe ../windows/pamhyr-windows.zip ../linux/pamhyr-gnulinux.tar.xz"
+fi
+
+clamscan $OPTS $FILES | tee clamav.log
+
+RES=$(cat clamav.log | grep "Infected files: 0")
+if [ -z "$RES" ]; then
+    echo "Infected files"
+    exit -1
+else
+    echo "OK"
+    exit 0
+fi

packages/debug.bat

@@ -0,0 +1,3 @@
+@echo off
+
+start cmd /c pamhyr.exe debug

packages/debug.sh

@@ -0,0 +1,3 @@
+#! /bin/sh
+
+./pamhyr debug

packages/make-windows-dir.bat

@@ -16,34 +16,35 @@ rem along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 @ECHO ON
 
-mkdir pamhyr\pamhyr\_internal
+mkdir pamhyr\_internal
-xcopy /s /e /y dist\pamhyr pamhyr\pamhyr
+xcopy /s /e /y dist\pamhyr pamhyr
 
 rem Copy data
-mkdir pamhyr\pamhyr\_internal\lang
+mkdir pamhyr\_internal\lang
-mkdir pamhyr\pamhyr\_internal\View\ui\ressources
+mkdir pamhyr\_internal\View\ui\ressources
-mkdir pamhyr\pamhyr\_internal\View\ui\Widgets
+mkdir pamhyr\_internal\View\ui\Widgets
 
 rem UI
-copy /y ..\src\View\ui\ressources\ pamhyr\pamhyr\_internal\View\ui\ressources
+copy /y ..\src\View\ui\ressources\ pamhyr\_internal\View\ui\ressources
-copy /y ..\src\View\ui\Widgets\*.ui pamhyr\pamhyr\_internal\View\ui\Widgets
+copy /y ..\src\View\ui\Widgets\*.ui pamhyr\_internal\View\ui\Widgets
-copy /y ..\src\View\ui\*.ui pamhyr\pamhyr\_internal\View\ui\
+copy /y ..\src\View\ui\*.ui pamhyr\_internal\View\ui\
 
 rem Lang
-copy /y ..\src\lang\*.qm pamhyr\pamhyr\_internal\lang\
+copy /y ..\src\lang\*.qm pamhyr\_internal\lang\
 
 rem Information
-copy /y ..\VERSION pamhyr\pamhyr\_internal
+copy /y ..\VERSION pamhyr\_internal
-copy /y ..\AUTHORS pamhyr\pamhyr\_internal
+copy /y ..\AUTHORS pamhyr\_internal
-copy /y ..\LICENSE pamhyr\pamhyr\_internal
+copy /y ..\LICENSE pamhyr\_internal
-copy /y ..\src\motd.txt pamhyr\pamhyr\_internal
+copy /y ..\src\motd.txt pamhyr\_internal
 
 rem MAGE
-mkdir pamhyr\mage
+mkdir pamhyr\mage8
-copy /y ..\mage-windows\mage.exe pamhyr\mage\
+copy /y ..\mage8-windows\mage.exe pamhyr\mage8\
-copy /y ..\mage-windows\mage_extraire.exe pamhyr\mage\
+copy /y ..\mage8-windows\mage_as7.exe pamhyr\mage8\
-copy /y ..\mage-windows\mailleurTT.exe pamhyr\mage\
+copy /y ..\mage8-windows\mage_extraire.exe pamhyr\mage8\
-copy /y ..\mage-windows\libbief.dll pamhyr\mage\
+copy /y ..\mage8-windows\mailleurTT.exe pamhyr\mage8\
+copy /y ..\mage8-windows\libbief.dll pamhyr\mage8\
 
 rem Copy tests_cases
 mkdir pamhyr\tests_cases

packages/pamhyr.nsi

@@ -3,9 +3,10 @@
 !define LIC_NAME "LICENSE"
 !define APP_NAME "PAMHYR"
 
+Icon "pamhyr\_internal\View\ui\ressources\icon.ico"
 Name "Pamhyr2"
 OutFile "pamhyr-windows.exe"
-LicenseData "pamhyr\pamhyr\_internal\LICENSE"
+LicenseData "pamhyr\_internal\LICENSE"
 LicenseText "I Agree"
 
 RequestExecutionLevel admin
@@ -41,12 +42,12 @@ SectionEnd
 Section "Start Menu Shortcuts"
   CreateDirectory "$SMPROGRAMS\Pamhyr2"
   CreateShortcut "$SMPROGRAMS\Pamhyr2\Uninstall.lnk" "$INSTDIR\uninstall.exe"
-  CreateShortcut "$SMPROGRAMS\Pamhyr2\Pamhyr2.lnk" "$INSTDIR\pamhyr\pamhyr.exe"
+  CreateShortcut "$SMPROGRAMS\Pamhyr2\Pamhyr2.lnk" "$INSTDIR\pamhyr.exe"
 SectionEnd
 
 Section "Desktop Shortcuts"
   SetShellVarContext all
-  CreateShortcut "$desktop\Pamhyr2.lnk" "$instdir\pamhyr\pamhyr.exe"
+  CreateShortcut "$desktop\Pamhyr2.lnk" "$instdir\pamhyr.exe"
 SectionEnd
 
 Section "Uninstall"

requirements.txt

@@ -4,9 +4,11 @@ PyQt5-sip==12.12.2
 #PyQtWebEngine==5.15.6
 QScintilla>=2.14.1
 pyqtgraph>=0.12.1
-matplotlib>=3.4.1
+matplotlib>=3.7.1
 numpy>=1.24.2
 colorama>=0.4.3
 pyinstaller>=5.11.0
 shapely>=2.0.1
 lxml>=4.9.3
+platformdirs>=4.2.0
+pyshp>=2.3.1

src/Checker/Checker.py

@@ -1,5 +1,5 @@
 # Checker.py -- Pamhyr abstract checker class
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -16,23 +16,53 @@
 
 # -*- coding: utf-8 -*-
 
+import logging
+
 from enum import Enum
 
+from Modules import Modules
 from Model.Except import NotImplementedMethodeError
 
+logger = logging.getLogger()
+
 
 class STATUS(Enum):
-    UNKNOWN = -1
     OK = 0
     WARNING = 1
     ERROR = 2
+    UNKNOWN = 999
+
+    def __eq__(self, y):
+        return self.value == y.value
+
+    def __gt__(self, y):
+        return self.value > y.value
+
+    def __or__(self, y):
+        v = [self, y]
+        r = self.OK
+
+        if self.UNKNOWN in v:
+            r = self.UNKNOWN
+        if self.ERROR in v:
+            r = self.ERROR
+        if self.WARNING in v:
+            r = self.WARNING
+
+        logger.debug(f"CHECKER: STATUS: {self} | {y} = {r}")
+        return r
 
 
 class AbstractModelChecker(object):
     def __init__(self):
         self._name = ""
         self._description = ""
+        self._solver = "study"
+        self._modules = Modules.NONE
 
+        self.reset()
+
+    def reset(self):
         self._status = STATUS.UNKNOWN
         self._summary = "Unknown"
 
@@ -62,6 +92,21 @@ class AbstractModelChecker(object):
     def is_error(self):
         return self._status == STATUS.ERROR
 
+    # Basic check
+    def basic_check(self, study):
+        if study is None:
+            self._status = STATUS.ERROR
+            self._summary = "invalid_study"
+            return False
+
+        river = study.river
+        if river is None:
+            self._status = STATUS.ERROR
+            self._summary = "no_river_found"
+            return False
+
+        return True
+
     # Abstract function
 
     def _run(self, study):

src/Checker/Mage.py

@@ -1,5 +1,5 @@
 # Mage.py -- Pamhyr MAGE checkers
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -23,6 +23,8 @@ from tools import flatten, timer
 
 from PyQt5.QtCore import QCoreApplication
 
+from Modules import Modules
+
 from Checker.Checker import AbstractModelChecker, STATUS
 from Checker.Study import StudyGeometryChecker
 
@@ -30,7 +32,7 @@ _translate = QCoreApplication.translate
 
 
 class MageNetworkGraphChecker(AbstractModelChecker):
-    def __init__(self, connectivity=True):
+    def __init__(self, connectivity=True, version="mage8"):
         super(MageNetworkGraphChecker, self).__init__()
 
         self._mode_conn = connectivity
@@ -44,6 +46,8 @@ class MageNetworkGraphChecker(AbstractModelChecker):
             "Checker", f"Mage network graph {mode} checker")
         self._description = _translate(
             "Checker", "Check if the network graph is valid")
+        self._solver = version
+        self._modules = Modules.NETWORK
 
     @timer
     def _connectivity(self, summary, status, graph):
@@ -199,15 +203,18 @@ class MageNetworkGraphChecker(AbstractModelChecker):
 
 
 class MageGeometryGuideLineChecker(StudyGeometryChecker):
-    def __init__(self):
+    def __init__(self, version="mage8"):
         super(MageGeometryGuideLineChecker, self).__init__()
 
-        self._name = _translate("Checker", "Mage geometry guide line checker")
+        self._name = _translate("Checker", "Mage geometry guideline checker")
         self._description = _translate(
             "Checker",
-            "Check if exists geometry guide line is correctly defined \
+            "Check if exists geometry guidelines are correctly defined \
-for each reaches of the study"
+for each reach"
         )
+        self._solver = version
+        self._modules = Modules.GEOMETRY
+
         self._reachs = []
 
     def run(self, study):
@@ -234,7 +241,7 @@ for each reaches of the study"
             for profile in profiles:
                 if not profile.has_standard_named_points():
                     self._status = STATUS.WARNING
-                    self._summary = "no_standard_guileline_defined"
+                    self._summary = "no_standard_guideline_defined"
                     return False
 
         for gl in gls[1:]:

src/Checker/Study.py

@@ -1,5 +1,5 @@
 # Study.py -- Pamhyr study checkers
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -17,33 +17,34 @@
 # -*- coding: utf-8 -*-
 
 import time
+import logging
+from functools import reduce
 
 from PyQt5.QtCore import QCoreApplication
 
+from Modules import Modules
 from Checker.Checker import AbstractModelChecker, STATUS
 
 _translate = QCoreApplication.translate
 
+logger = logging.getLogger()
+
 
 class StudyNetworkReachChecker(AbstractModelChecker):
     def __init__(self):
         super(StudyNetworkReachChecker, self).__init__()
 
-        self._name = _translate("Checker", "Study network reach checker")
+        self._name = _translate("Checker", "Study reach network checker")
         self._description = _translate(
-            "Checker", "Check if exists at least one reach for study")
+            "Checker", "Check if exists at least one reach exists"
+        )
+        self._modules = Modules.NETWORK
 
     def run(self, study):
-        if study is None:
+        if not self.basic_check(study):
-            self._status = STATUS.ERROR
-            self._summary = "invalid_study"
             return False
 
         river = study.river
-        if river is None:
-            self._status = STATUS.ERROR
-            self._summary = "no_river_found"
-            return False
 
         edges = list(filter(lambda e: e.is_enable(), river.edges()))
         if len(edges) == 0:
@@ -62,7 +63,10 @@ class StudyGeometryChecker(AbstractModelChecker):
 
         self._name = _translate("Checker", "Study geometry checker")
         self._description = _translate(
-            "Checker", "Check if exists geometry for each reach of study")
+            "Checker", "Check if the geometry of each reach exists"
+        )
+        self._modules = Modules.GEOMETRY
+
         self._reachs = []
 
     def run(self, study):
@@ -71,16 +75,10 @@ class StudyGeometryChecker(AbstractModelChecker):
         summary = "ok"
         status = STATUS.OK
 
-        if study is None:
+        if not self.basic_check(study):
-            self._status = STATUS.ERROR
-            self._summary = "invalid_study"
             return False
 
         river = study.river
-        if river is None:
-            self._status = STATUS.ERROR
-            self._summary = "no_river_found"
-            return False
 
         edges = river.enable_edges()
         if len(edges) == 0:
@@ -100,6 +98,124 @@ class StudyGeometryChecker(AbstractModelChecker):
         return ok
 
 
+class StudyInitialConditionsChecker(AbstractModelChecker):
+    def __init__(self):
+        super(StudyInitialConditionsChecker, self).__init__()
+
+        self._name = _translate("Checker", "Study initial conditions checker")
+        self._description = _translate(
+            "Checker", "Check initial conditions for each node of study"
+        )
+        self._modules = Modules.INITIAL_CONDITION
+
+    def run(self, study):
+        ok = True
+        nerror = 0
+        self._summary = "ok"
+        self._status = STATUS.OK
+
+        if not self.basic_check(study):
+            return False
+
+        for reach in study.river.enable_edges():
+            ok &= self.check_reach(study, reach.reach)
+
+        return ok
+
+    def check_reach(self, study, reach):
+        ok = True
+        river = study.river
+
+        if reach not in river.initial_conditions:
+            self._summary = "missing_initial_condition_defined"
+            self._status = STATUS.WARNING
+            return ok
+
+        ic = river.initial_conditions[reach]
+        len_ic = len(ic)
+        len_reach = len(reach)
+
+        if len_ic < len_reach:
+            self._summary = "initial_condition_missing_profile"
+            self._status = STATUS.WARNING
+
+        if len_ic > len_reach:
+            self._summary = "more_initial_condition_than_profile"
+            self._status = STATUS.ERROR
+            ok = False
+
+        return ok
+
+
+class StudyBoundaryConditionChecker(AbstractModelChecker):
+    def __init__(self):
+        super(StudyBoundaryConditionChecker, self).__init__()
+
+        self._name = _translate("Checker", "Study boundary conditions checker")
+        self._description = _translate(
+            "Checker", "Check boundary conditions for each node of study"
+        )
+        self._modules = Modules.BOUNDARY_CONDITION
+
+    def run(self, study):
+        ok = True
+        nerror = 0
+        self._summary = "ok"
+        self._status = STATUS.OK
+
+        if not self.basic_check(study):
+            return False
+
+        ok = self.check_liquid(study)
+
+        return ok
+
+    def check_liquid(self, study):
+        river = study.river
+
+        bcs = river.boundary_condition.get_tab('liquid')
+        if len(bcs) == 0:
+            self._status = STATUS.ERROR
+            self._summary = "no_boundary_condition_defined"
+            return False
+
+        upstream, downstream = reduce(
+            lambda acc, n: (
+                acc[0] + [n] if river.is_upstream_node(n) else acc[0],
+                acc[1] + [n] if river.is_downstream_node(n) else acc[1],
+            ),
+            filter(
+                lambda n: river.is_enable_node(n),
+                river.nodes()
+            ),
+            ([], [])
+        )
+
+        bcs_nodes = set(map(lambda bc: bc.node, bcs))
+
+        upstream_ok = self.check_liquid_all_node_has_bc(
+            bcs_nodes, upstream
+        )
+        downstream_ok = self.check_liquid_all_node_has_bc(
+            bcs_nodes, downstream
+        )
+
+        ok = upstream_ok and downstream_ok
+
+        if not ok:
+            self._status = STATUS.ERROR
+            self._summary = "no_boundary_condition_at_boundary_node"
+
+        return ok
+
+    def check_liquid_all_node_has_bc(self, bcs_nodes, nodes):
+        return reduce(
+            lambda acc, n: (acc and (n in bcs_nodes)),
+            nodes,
+            True
+        )
+
+
 class DummyOK(AbstractModelChecker):
     def __init__(self):
         super(DummyOK, self).__init__()

src/Meshing/AMeshingTool.py

@@ -1,5 +1,5 @@
 # AMeshingTool.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Meshing/Mage.py

@@ -1,5 +1,5 @@
 # Mage.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -30,7 +30,7 @@ from ctypes import (
 )
 from PyQt5.QtCore import QProcess
 
-from tools import logger_color_red, logger_color_reset
+from tools import logger_color_red, logger_color_reset, logger_exception
 from Meshing.AMeshingTool import AMeshingTool
 
 logger = logging.getLogger()
@@ -65,6 +65,10 @@ class MeshingWithMage(AMeshingTool):
             )
         )
 
+    @classmethod
+    def _path(cls):
+        return cls._exe_path()
+
     def _init_c_init_bief_from_geo_file(self):
         self._c_init_bief_from_geo_file = getattr(
             self._bief_lib, 'c_init_bief_from_geo_file'
@@ -274,15 +278,27 @@ class MeshingWithMageMailleurTT(AMeshingTool):
         return os.path.abspath(
             os.path.join(
                 os.path.dirname(__file__),
-                "..", "..", "..", "mage", f"mailleurTT{ext}"
+                "..", "..", "mage8", f"mailleurTT{ext}"
             )
         )
 
+    @classmethod
+    def _path(cls):
+        return cls._exe_path()
+
     ###########
     # Meshing #
     ###########
 
-    def meshing(self, reach, step: float = 50):
+    def meshing(self, reach,
+                step: float = 50,
+                limites=[-1, -1],
+                origin=0,
+                directrices=['un', 'np'],
+                lplan: bool = False,
+                lm: int = 3,
+                linear: bool = False,
+                origin_value=0.0):
         if reach is None or len(reach.profiles) == 0:
             return reach
 
@@ -294,19 +310,133 @@ class MeshingWithMageMailleurTT(AMeshingTool):
             proc = QProcess()
             proc.setWorkingDirectory(tmp)
 
-            logger.debug(f"mailleurTT '{st_file}, {m_file}, {str(step)}'")
+            # Mage section index start at 1
+            origin += 1
+            limites[0] += 1
+            limites[1] += 1
+
+            lplan = 1 if lplan else 0
+            linear = 1 if linear else 0
+
+            logger.info(
+                f"! {self._exe_path()} " +
+                f"{st_file} {m_file} " +
+                f"mesh " +
+                f"{str(step)} " +
+                f"{limites[0]} {limites[1]} " +
+                f"{directrices[0]} {directrices[1]} " +
+                f"{lplan} {lm} {linear} " +
+                f"{origin} "
+            )
             proc.start(
-                self._exe_path(), [st_file, m_file, str(step)]
+                self._exe_path(),
+                list(
+                    map(
+                        str,
+                        [
+                            st_file, m_file,
+                            "mesh", step,
+                            limites[0], limites[1],
+                            directrices[0], directrices[1],
+                            lplan, lm, linear, origin, origin_value
+                        ]
+                    )
+                )
             )
             proc.waitForFinished()
 
-            errors = proc.readAllStandardError()
+            if proc.exitCode() != 0:
-            if len(errors) != 0:
+                logger.error(
+                    f"{logger_color_red()}" +
+                    f"MailleurTT error: {proc.exitCode()}" +
+                    f"{logger_color_reset()}"
+                )
+                outputs = proc.readAllStandardOutput()
+                logger.debug(outputs)
+
+                errors = proc.readAllStandardError()
                 logger.error(
                     f"{logger_color_red()}{errors}{logger_color_reset()}"
                 )
-            else:
+                return reach
-                self.import_m_file(reach, m_file)
+
+            self.import_m_file(reach, m_file)
+            return reach
+
+    def update_rk(self, reach,
+                  step: float = 50,
+                  limites=[-1, -1],
+                  origin=0,
+                  directrices=['un', 'np'],
+                  lplan: bool = False,
+                  lm: int = 3,
+                  linear: bool = False,
+                  origin_value=0.0,
+                  orientation=0):
+        if reach is None or len(reach.profiles) == 0:
+            return reach
+
+        with tempfile.TemporaryDirectory() as tmp:
+            logger.debug(f"temp file: {tmp}")
+            st_file = self.export_reach_to_st(reach, tmp)
+            m_file = st_file.rsplit(".ST", 1)[0] + ".M"
+
+            os.sync()
+
+            proc = QProcess()
+            proc.setWorkingDirectory(tmp)
+
+            # Mage section indices start at 1
+            origin += 1
+            limites[0] += 1
+            limites[1] += 1
+
+            lplan = 1 if lplan else 0
+            linear = 1 if linear else 0
+
+            logger.info(
+                f"! {self._exe_path()} " +
+                f"{st_file} {m_file} " +
+                f"update_rk " +
+                f"{str(step)} " +
+                f"{limites[0]} {limites[1]} " +
+                f"{directrices[0]} {directrices[1]} " +
+                f"{orientation} {lm} {linear} " +
+                f"{origin} "
+            )
+            proc.start(
+                self._exe_path(),
+                list(
+                    map(
+                        str,
+                        [
+                            st_file, m_file,
+                            "update_rk", step,
+                            limites[0], limites[1],
+                            directrices[0], directrices[1],
+                            orientation, lm, linear, origin, origin_value
+                        ]
+                    )
+                )
+            )
+            proc.waitForFinished()
+
+            if proc.exitCode() != 0:
+                logger.error(
+                    f"{logger_color_red()}" +
+                    f"MailleurTT error: {proc.exitCode()}" +
+                    f"{logger_color_reset()}"
+                )
+                outputs = proc.readAllStandardOutput()
+                logger.debug(outputs)
+
+                errors = proc.readAllStandardError()
+                logger.error(
+                    f"{logger_color_red()}{errors}{logger_color_reset()}"
+                )
+                return reach
+
+            self.import_m_file(reach, m_file)
             return reach
 
     def export_reach_to_st(self, reach, tmp):
@@ -318,7 +448,9 @@ class MeshingWithMageMailleurTT(AMeshingTool):
         return tmp_st
 
     def import_m_file(self, reach, m):
-        reach.purge()
+        if os.path.exists(m):
-
+            reach.purge()
-        logger.debug(f"meshing: Import geometry from {m}")
+            logger.debug(f"meshing: Import geometry from {m}")
-        reach.import_geometry(m)
+            reach.import_geometry(m)
+        else:
+            logger.error(f"meshing: Meshed geometry file {m} do not exists")

src/Meshing/__init__.py

@@ -1,5 +1,5 @@
 # __init__.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Meshing/test_Meshing.py

@@ -1,5 +1,5 @@
 # test_Model.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -25,9 +25,10 @@ from Model.Saved import SavedStatus
 from Model.Study import Study
 from Model.River import River
 
-from Meshing.Mage import MeshingWithMage
+from Meshing.Mage import MeshingWithMage, MeshingWithMageMailleurTT
 
 mage_mesher = os.path.exists(MeshingWithMage._lib_path())
+mage_mesher_TT = os.path.exists(MeshingWithMageMailleurTT._exe_path())
 
 
 class MeshingTestCase(unittest.TestCase):
@@ -35,3 +36,8 @@ class MeshingTestCase(unittest.TestCase):
     def test_create_meshingtool_mage(self):
         mesher = MeshingWithMage()
         self.assertNotEqual(mesher, None)
+
+    @unittest.skipIf(not mage_mesher_TT, "mailleurTT is not available")
+    def test_create_meshingtool_mageTT(self):
+        mesher = MeshingWithMageMailleurTT()
+        self.assertNotEqual(mesher, None)

src/Model/AdditionalFile/AddFile.py

@@ -0,0 +1,178 @@
+# AddFile.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+from functools import reduce
+
+from tools import trace, timer
+
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Except import NotImplementedMethodeError
+
+
+class AddFile(SQLSubModel):
+    _sub_classes = []
+    _id_cnt = 0
+
+    def __init__(self, id: int = -1, enabled=True,
+                 name="", path="", text="",
+                 status=None):
+        super(AddFile, self).__init__()
+
+        if id == -1:
+            self.id = AddFile._id_cnt
+        else:
+            self.id = id
+
+        self._status = status
+
+        self._enabled = enabled
+        self._name = f"File {self.id}" if name == "" else name
+        self._path = path
+        self._text = text
+
+        AddFile._id_cnt = max(id, AddFile._id_cnt+1)
+
+    def __getitem__(self, key):
+        value = None
+
+        if key == "enabled":
+            value = self._enabled
+        elif key == "name":
+            value = self._name
+        elif key == "path":
+            value = self._path
+        elif key == "text":
+            value = self._text
+
+        return value
+
+    def __setitem__(self, key, value):
+        if key == "enabled":
+            self._enabled = value
+        elif key == "name":
+            self._name = value
+        elif key == "path":
+            self._path = value
+        elif key == "text":
+            self._text = value
+
+        self._status.modified()
+
+    @property
+    def enabled(self):
+        return self._enabled
+
+    @enabled.setter
+    def enabled(self, enabled):
+        self._enabled = enabled
+        self._status.modified()
+
+    def is_enabled(self):
+        return self._enabled
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+        self._status.modified()
+
+    @property
+    def path(self):
+        return self._path
+
+    @path.setter
+    def path(self, path):
+        self._path = path
+        self._status.modified()
+
+    @property
+    def text(self):
+        return self._text
+
+    @text.setter
+    def text(self, text):
+        self._text = text
+        self._status.modified()
+
+    @classmethod
+    def _db_create(cls, execute):
+        execute("""
+          CREATE TABLE additional_files(
+            id INTEGER NOT NULL PRIMARY KEY,
+            enabled BOOLEAN NOT NULL,
+            name TEXT NOT NULL,
+            path TEXT NOT NULL,
+            text TEXT NOT NULL
+          )
+        """)
+
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 8:
+                cls._db_create(execute)
+
+        return True
+
+    @classmethod
+    def _db_load(cls, execute, data=None):
+        new = []
+
+        table = execute(
+            "SELECT id, enabled, name, path, text " +
+            "FROM additional_files"
+        )
+
+        for row in table:
+            it = iter(row)
+
+            id = next(it)
+            enabled = (next(it) == 1)
+            name = next(it)
+            path = next(it)
+            text = next(it)
+
+            f = cls(
+                id=id, enabled=enabled, name=name, path=path, text=text,
+                status=data['status']
+            )
+
+            new.append(f)
+
+        return new
+
+    def _db_save(self, execute, data=None):
+        sql = (
+            "INSERT INTO " +
+            "additional_files(id, enabled, name, path, text) " +
+            "VALUES (" +
+            f"{self.id}, {self._enabled}, " +
+            f"'{self._db_format(self._name)}', " +
+            f"'{self._db_format(self._path)}', " +
+            f"'{self._db_format(self._text)}'" +
+            ")"
+        )
+        execute(sql)
+
+        return True

src/Model/AdditionalFile/AddFileList.py

@@ -0,0 +1,56 @@
+# AddFileList.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+from tools import trace, timer
+
+from Model.Except import NotImplementedMethodeError
+from Model.Tools.PamhyrList import PamhyrModelList
+from Model.AdditionalFile.AddFile import AddFile
+
+
+class AddFileList(PamhyrModelList):
+    _sub_classes = [AddFile]
+
+    @classmethod
+    def _db_load(cls, execute, data=None):
+        new = cls(status=data["status"])
+
+        new._lst = AddFile._db_load(execute, data)
+
+        return new
+
+    def _db_save(self, execute, data=None):
+        ok = True
+
+        # Delete previous data
+        execute("DELETE FROM additional_files")
+
+        for af in self._lst:
+            ok &= af._db_save(execute, data)
+
+        return ok
+
+    @property
+    def files(self):
+        return self.lst
+
+    def new(self, index):
+        n = AddFile(status=self._status)
+        self.insert(index, n)
+        self._status.modified()
+        return n

src/Model/BoundaryCondition/BoundaryCondition.py

@@ -1,5 +1,5 @@
 # BoundaryCondition.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -18,7 +18,12 @@
 
 import logging
 
-from tools import trace, timer, old_pamhyr_date_to_timestamp
+from tools import (
+    trace, timer,
+    old_pamhyr_date_to_timestamp,
+    date_iso_to_timestamp,
+    date_dmy_to_timestamp,
+)
 
 from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import NotImplementedMethodeError
@@ -189,6 +194,10 @@ class BoundaryCondition(SQLSubModel):
     @classmethod
     def time_convert(cls, data):
         if type(data) is str:
+            if data.count("-") == 2:
+                return date_iso_to_timestamp(data)
+            if data.count("/") == 2:
+                return date_dmy_to_timestamp(data)
             if data.count(":") == 3:
                 return old_pamhyr_date_to_timestamp(data)
             if data.count(":") == 2:
@@ -200,6 +209,9 @@ class BoundaryCondition(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"B{self.id + 1}"
+
         return self._name
 
     @name.setter
@@ -303,6 +315,9 @@ class BoundaryCondition(SQLSubModel):
             self._data.sort(reverse=_reverse, key=key)
         self._status.modified()
 
+    def index(self, bc):
+        self._data.index(bc)
+
     def get_i(self, index):
         return self.data[index]
 

src/Model/BoundaryCondition/BoundaryConditionList.py

@@ -1,5 +1,5 @@
 # BoundaryConditionList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/BoundaryCondition/BoundaryConditionTypes.py

@@ -1,5 +1,5 @@
 # BoundaryConditionTypes.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Except.py

@@ -1,5 +1,5 @@
 # Except.py -- Pamhyr model exceptions
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -21,7 +21,7 @@ from PyQt5.QtCore import (
 )
 
 from PyQt5.QtWidgets import (
-    QApplication, QMessageBox,
+    QApplication, QMessageBox, QLabel,
 )
 
 _translate = QCoreApplication.translate
@@ -34,6 +34,7 @@ _translate = QCoreApplication.translate
 def exception_message_box(exception):
     msg = QMessageBox()
     msg.setIcon(QMessageBox.Critical)
+    msg.findChild(QLabel, "qt_msgbox_label").setFixedWidth(384)
 
     msg.setText("Exception :")
     msg.setInformativeText(f"{exception}")

src/Model/Friction/Friction.py

@@ -1,5 +1,5 @@
 # Friction.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -26,15 +26,25 @@ logger = logging.getLogger()
 
 
 class Friction(SQLSubModel):
-    def __init__(self, name: str = "", status=None):
+    _id_cnt = 0
+
+    def __init__(self, id: int = -1, name: str = "",
+                 status=None):
         super(Friction, self).__init__()
 
         self._status = status
 
+        if id == -1:
+            self.id = Friction._id_cnt
+        else:
+            self.id = id
+
+        Friction._id_cnt = max(self.id, Friction._id_cnt+1)
+
         self._name = name
         self._edge = None
-        self._begin_kp = 0.0
+        self._begin_rk = 0.0
-        self._end_kp = 0.0
+        self._end_rk = 0.0
         self._begin_strickler = None
         self._end_strickler = None
 
@@ -42,13 +52,13 @@ class Friction(SQLSubModel):
     def _db_create(cls, execute):
         execute("""
           CREATE TABLE friction(
-            id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
+            id INTEGER NOT NULL PRIMARY KEY,
-            ind INTERGER NOT NULL,
+            ind INTEGER NOT NULL,
-            begin_kp REAL NOT NULL,
+            begin_rk REAL NOT NULL,
-            end_kp REAL NOT NULL,
+            end_rk REAL NOT NULL,
             reach INTEGER NOT NULL,
-            begin_strickler INTERGER,
+            begin_strickler INTEGER NOT NULL,
-            end_strickler INTERGER,
+            end_strickler INTEGER NOT NULL,
             FOREIGN KEY(reach) REFERENCES river_reach(id),
             FOREIGN KEY(begin_strickler) REFERENCES stricklers(id),
             FOREIGN KEY(end_strickler) REFERENCES stricklers(id)
@@ -59,6 +69,12 @@ class Friction(SQLSubModel):
 
     @classmethod
     def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 11:
+                execute("ALTER TABLE friction RENAME COLUMN begin_kp TO begin_rk")
+                execute("ALTER TABLE friction RENAME COLUMN end_kp TO end_rk")
+
         return True
 
     @classmethod
@@ -70,28 +86,30 @@ class Friction(SQLSubModel):
         stricklers = data["stricklers"].stricklers
 
         table = execute(
-            "SELECT ind, begin_kp, end_kp, begin_strickler, end_strickler " +
+            "SELECT id, ind, begin_rk, end_rk, " +
+            "begin_strickler, end_strickler " +
             f"FROM friction WHERE reach = {reach.id}"
         )
 
         for row in table:
-            ind = row[0]
+            id = row[0]
+            ind = row[1]
             # Get stricklers
-            if int(row[3]) == -1:
+            if int(row[4]) == -1:
                 bs = None
             else:
-                bs = next(filter(lambda s: s.id == row[3], stricklers))
+                bs = next(filter(lambda s: s.id == row[4], stricklers))
 
-            if int(row[4]) == -1:
+            if int(row[5]) == -1:
                 es = None
             else:
-                es = next(filter(lambda s: s.id == row[4], stricklers))
+                es = next(filter(lambda s: s.id == row[5], stricklers))
 
             # Create friction
             sec = cls(status=status)
             sec.edge = reach
-            sec.begin_kp = row[1]
+            sec.begin_rk = row[2]
-            sec.end_kp = row[2]
+            sec.end_rk = row[3]
             sec.begin_strickler = bs
             sec.end_strickler = es
 
@@ -112,10 +130,11 @@ class Friction(SQLSubModel):
 
         execute(
             "INSERT INTO " +
-            "friction(ind, begin_kp, end_kp, " +
+            "friction(id, ind, begin_rk, end_rk, " +
             "reach, begin_strickler, end_strickler) " +
             "VALUES (" +
-            f"{ind}, {self._begin_kp}, {self._end_kp}, " +
+            f"{self.id}, {ind}, " +
+            f"{self._begin_rk}, {self._end_rk}, " +
             f"{self._edge.id}, " +
             f"{b_s_id}, {e_s_id}" +
             ")"
@@ -144,10 +163,10 @@ class Friction(SQLSubModel):
     def edge(self, edge):
         self._edge = edge
         if (edge is not None and
-            self._begin_kp == 0.0 and
+            self._begin_rk == 0.0 and
-                self._end_kp == 0.0):
+                self._end_rk == 0.0):
-            self._begin_kp = self._edge.reach.get_kp_min()
+            self._begin_rk = self._edge.reach.get_rk_min()
-            self._end_kp = self._edge.reach.get_kp_max()
+            self._end_rk = self._edge.reach.get_rk_max()
         self._status.modified()
 
     def has_edge(self):
@@ -163,39 +182,47 @@ class Friction(SQLSubModel):
         return self.has_edge() and self.has_coefficient()
 
     @property
-    def begin_kp(self):
+    def begin_rk(self):
-        return self._begin_kp
+        return self._begin_rk
 
-    @begin_kp.setter
+    @begin_rk.setter
-    def begin_kp(self, begin_kp):
+    def begin_rk(self, begin_rk):
         if self._edge is None:
-            self._begin_kp = begin_kp
+            self._begin_rk = begin_rk
         else:
-            _min = self._edge.reach.get_kp_min()
+            _min = self._edge.reach.get_rk_min()
-            _max = self._edge.reach.get_kp_max()
+            _max = self._edge.reach.get_rk_max()
 
-            if _min <= begin_kp <= _max:
+            if _min <= begin_rk <= _max:
-                self._begin_kp = begin_kp
+                self._begin_rk = begin_rk
 
         self._status.modified()
 
     @property
-    def end_kp(self):
+    def end_rk(self):
-        return self._end_kp
+        return self._end_rk
 
-    @end_kp.setter
+    @end_rk.setter
-    def end_kp(self, end_kp):
+    def end_rk(self, end_rk):
         if self._edge is None:
-            self._end_kp = end_kp
+            self._end_rk = end_rk
         else:
-            _min = self._edge.reach.get_kp_min()
+            _min = self._edge.reach.get_rk_min()
-            _max = self._edge.reach.get_kp_max()
+            _max = self._edge.reach.get_rk_max()
 
-            if _min <= end_kp <= _max:
+            if _min <= end_rk <= _max:
-                self._end_kp = end_kp
+                self._end_rk = end_rk
 
         self._status.modified()
 
+    def __contains__(self, rk):
+        return self.contains_rk(rk)
+
+    def contains_rk(self, rk):
+        return (
+            self._begin_rk <= rk <= self._end_rk
+        )
+
     @property
     def begin_strickler(self):
         return self._begin_strickler

src/Model/Friction/FrictionList.py

@@ -1,5 +1,5 @@
 # FrictionList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -44,7 +44,7 @@ class FrictionList(PamhyrModelList):
             logger.info(f"Update friction TABLE from {version}")
             cls._db_update_0_0_1(execute, version)
 
-        return True
+        return cls._update_submodel(execute, version)
 
     @classmethod
     def _db_load(cls, execute, data=None):

src/Model/Geometry/Point.py

@@ -1,5 +1,5 @@
 # Point.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Geometry/PointXY.py

@@ -1,5 +1,5 @@
 # PointXY.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Geometry/PointXYZ.py

@@ -1,5 +1,5 @@
 # PointXYZ.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -47,7 +47,7 @@ class PointXYZ(Point, SQLSubModel):
             z INTEGER NOT NULL,
             profile INTEGER NOT NULL,
             sl INTEGER,
-            FOREIGN KEY(profile) REFERENCES profileXYZ(id),
+            FOREIGN KEY(profile) REFERENCES geometry_profileXYZ(id),
             FOREIGN KEY(sl) REFERENCES sedimentary_layer(id)
           )
         """)
@@ -192,6 +192,22 @@ class PointXYZ(Point, SQLSubModel):
     def dist(self, p2):
         return PointXYZ.distance(self, p2)
 
+    def dist_2d(self, p2):
+        return PointXYZ.distance_2d(self, p2)
+
+    @staticmethod
+    def distance_2d(p1, p2):
+        """Euclidean distance between p1 and p2.
+
+        Args:
+            p1: A XYZ Point
+            p2: A XYZ Point
+
+        Returns:
+            Euclidean 2D distance between the two points
+        """
+        return dist((p1.x, p1.y), (p2.x, p2.y))
+
     @staticmethod
     def distance(p1, p2):
         """Euclidean distance between p1 and p2.
@@ -201,6 +217,14 @@ class PointXYZ(Point, SQLSubModel):
             p2: A XYZ Point
 
         Returns:
-            Euclidean distance between the two points
+            Euclidean 3D distance between the two points
         """
         return dist((p1.x, p1.y, p1.z), (p2.x, p2.y, p2.z))
+
+    @staticmethod
+    def areatriangle3d(p1, p2, p3):
+        a = PointXYZ.distance(p1, p2)
+        b = PointXYZ.distance(p2, p3)
+        c = PointXYZ.distance(p3, p1)
+        s = (a + b + c) / 2
+        return (s*(s-a) * (s-b)*(s-c)) ** 0.5

src/Model/Geometry/Profile.py

@@ -1,5 +1,5 @@
 # Profile.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -19,6 +19,7 @@
 import logging
 
 from tools import timer
+from shapely import geometry
 
 from Model.Geometry.Point import Point
 from Model.Except import NotImplementedMethodeError
@@ -30,7 +31,7 @@ class Profile(object):
     _id_cnt = 0
 
     def __init__(self, id: int = -1, num: int = 0,
-                 kp: float = 0.0, name: str = "",
+                 rk: float = 0.0, name: str = "",
                  code1: int = 0, code2: int = 0,
                  _type: str = "", reach=None,
                  status=None):
@@ -48,7 +49,7 @@ class Profile(object):
         self._num = int(num)
         self._code1 = int(code1)
         self._code2 = int(code2)
-        self._kp = float(kp)
+        self._rk = float(rk)
         self._name = str(name)
         self._reach = reach
         self._sl = None
@@ -135,16 +136,16 @@ class Profile(object):
         return len(self.points)
 
     @property
-    def kp(self):
+    def rk(self):
         """
         Returns:
             Kilometer point.
         """
-        return self._kp
+        return self._rk
 
-    @kp.setter
+    @rk.setter
-    def kp(self, value: float):
+    def rk(self, value: float):
-        self._kp = float(value)
+        self._rk = float(value)
         self._status.modified()
 
     @property
@@ -295,6 +296,11 @@ class Profile(object):
         )
         self._status.modified()
 
+    @timer
+    def reverse(self):
+        self._points.reverse()
+        self._status.modified()
+
     # Sediment Layers
 
     def get_sl(self):
@@ -341,3 +347,12 @@ class Profile(object):
     # Abstract method for width approximation
     def get_water_limits(self, z):
         raise NotImplementedMethodeError(self, self.get_water_limits)
+
+    def wet_points(self, z):
+        raise NotImplementedMethodeError(self, self.wet_point)
+
+    def wet_perimeter(self, z):
+        raise NotImplementedMethodeError(self, self.wet_perimeter)
+
+    def wet_area(self, z):
+        raise NotImplementedMethodeError(self, self.wet_area)

src/Model/Geometry/ProfileXYZ.py

@@ -1,5 +1,5 @@
 # ProfileXYZ.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -22,6 +22,7 @@ from typing import List
 from functools import reduce
 
 from tools import timer
+from shapely import geometry
 
 from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import ClipboardFormatError
@@ -40,7 +41,7 @@ class ProfileXYZ(Profile, SQLSubModel):
     def __init__(self,
                  id: int = -1,
                  name: str = "",
-                 kp: float = 0.,
+                 rk: float = 0.,
                  reach=None,
                  num=0,
                  nb_point: int = 0,
@@ -52,7 +53,7 @@ class ProfileXYZ(Profile, SQLSubModel):
             num: The number of this profile
             code1: The interpolation code 1
             code2: The interpolation code 2
-            kp: Kilometer point
+            rk: Kilometer point
             name: The name of profile
 
         Returns:
@@ -62,7 +63,7 @@ class ProfileXYZ(Profile, SQLSubModel):
             id=id,
             num=num,
             name=name,
-            kp=kp,
+            rk=rk,
             code1=code1, code2=code2,
             _type="XYZ",
             reach=reach,
@@ -77,7 +78,7 @@ class ProfileXYZ(Profile, SQLSubModel):
             ind INTEGER NOT NULL,
             name TEXT,
             reach INTEGER NOT NULL,
-            kp REAL NOT NULL,
+            rk REAL NOT NULL,
             num INTEGER NOT NULL,
             code1 INTEGER NOT NULL,
             code2 INTEGER NOT NULL,
@@ -93,7 +94,8 @@ class ProfileXYZ(Profile, SQLSubModel):
     def _db_update(cls, execute, version):
         major, minor, release = version.strip().split(".")
         if major == minor == "0":
-            if int(release) < 2:
+            rl = int(release)
+            if rl < 2:
                 execute(
                     """
                     ALTER TABLE geometry_profileXYZ
@@ -102,6 +104,14 @@ class ProfileXYZ(Profile, SQLSubModel):
                     """
                 )
 
+            if rl < 11:
+                execute(
+                    """
+                    ALTER TABLE geometry_profileXYZ
+                    RENAME COLUMN kp TO rk
+                    """
+                )
+
         return cls._update_submodel(execute, version)
 
     @classmethod
@@ -111,7 +121,7 @@ class ProfileXYZ(Profile, SQLSubModel):
         reach = data["reach"]
 
         table = execute(
-            "SELECT id, ind, name, kp, num, code1, code2, sl " +
+            "SELECT id, ind, name, rk, num, code1, code2, sl " +
             "FROM geometry_profileXYZ " +
             f"WHERE reach = {reach.id}"
         )
@@ -120,7 +130,7 @@ class ProfileXYZ(Profile, SQLSubModel):
             id = row[0]
             ind = row[1]
             name = row[2]
-            kp = row[3]
+            rk = row[3]
             num = row[5]
             code1 = row[5]
             code2 = row[6]
@@ -128,7 +138,7 @@ class ProfileXYZ(Profile, SQLSubModel):
 
             new = cls(
                 id=id, num=num,
-                name=name, kp=kp,
+                name=name, rk=rk,
                 code1=code1, code2=code2,
                 reach=reach,
                 status=status
@@ -158,10 +168,10 @@ class ProfileXYZ(Profile, SQLSubModel):
         sql = (
             "INSERT OR REPLACE INTO " +
             "geometry_profileXYZ(id, ind, name, reach, " +
-            "kp, num, code1, code2, sl) " +
+            "rk, num, code1, code2, sl) " +
             "VALUES (" +
             f"{self.id}, {ind}, '{self._db_format(self._name)}', " +
-            f"{self.reach.id}, {self.kp}, {self.num}, " +
+            f"{self.reach.id}, {self.rk}, {self.num}, " +
             f"{self.code1}, {self.code1}, {sl}" +
             ")"
         )
@@ -186,19 +196,19 @@ class ProfileXYZ(Profile, SQLSubModel):
         try:
             if len(header) == 0:
                 name = data[0]
-                kp = data[1]
+                rk = data[1]
                 reach = data[2]
                 status = data[3]
 
                 profile = cls(
                     id=-1,
                     name=name,
-                    kp=kp,
+                    rk=rk,
                     reach=reach,
                     status=status
                 )
             else:
-                valid_header = {'name', 'reach', 'kp', 'status'}
+                valid_header = {'name', 'reach', 'rk', 'status'}
                 d = {}
                 for i, v in enumerate(data):
                     h = header[i].strip().lower().split(' ')[0]
@@ -322,7 +332,7 @@ class ProfileXYZ(Profile, SQLSubModel):
             logger.debug(f"{e}")
             raise IndexError(
                 f"Invalid point name: {name} " +
-                f"for profile ({self.id}) kp = {self.kp}"
+                f"for profile ({self.id}) rk = {self.rk}"
             )
 
     def has_standard_named_points(self):
@@ -373,99 +383,13 @@ class ProfileXYZ(Profile, SQLSubModel):
         """
         return [x for x in lst if not np.isnan(x)]
 
-    def _first_point_not_nan(self):
+    def speed(self, q, z):
-        first_point = self.points[0]
+        area = self.wet_area(z)
 
-        for point in self.points:
+        if area == 0:
-            if not point.is_nan():
+            return 0
-                first_point = point
-                break
 
-        return first_point
+        return q / area
-
-    def _last_point_not_nan(self):
-        last_point = self.points[-1]
-
-        for point in self.points[::-1]:
-            if not point.is_nan():
-                last_point = point
-                break
-
-        return last_point
-
-    @timer
-    def get_station(self) -> np.ndarray:
-        """Projection of the points of the profile on a plane.
-
-        Args:
-            profile: The profile
-
-        Returns:
-            Projection of the points of the profile on a plane.
-        """
-        if self.nb_points < 3:
-            return None
-        else:
-            first_named_point = None
-            index_first_named_point = None
-            last_named_point = None
-
-            first_point_not_nan = self._first_point_not_nan()
-            last_point_not_nan = self._last_point_not_nan()
-
-            for index, point in enumerate(self.points):
-                if point.point_is_named():
-                    index_first_named_point = index
-                    first_named_point = point
-                    break
-
-            for point in reversed(self.points):
-                if point.point_is_named():
-                    last_named_point = point
-                    break
-
-            station = []
-            constant = 0.0
-
-            if (first_named_point is not None and
-                    last_named_point is not None):
-                if (first_named_point != last_named_point and
-                        first_named_point.x != last_named_point.x):
-                    vector = Vector1d(first_named_point, last_named_point)
-                    norm_dir_vec = vector.normalized_direction_vector()
-                else:
-                    vector = Vector1d(first_point_not_nan, last_point_not_nan)
-                    norm_dir_vec = vector.normalized_direction_vector()
-
-                for point in self.points:
-                    xi = point.x - first_named_point.x
-                    yi = point.y - first_named_point.y
-                    station_i = (norm_dir_vec[0] * xi +
-                                 norm_dir_vec[1] * yi)
-                    station.append(station_i)
-
-                constant = station[index_first_named_point]
-            elif first_named_point is None:
-                vector = Vector1d(first_point_not_nan, last_point_not_nan)
-                norm_dir_vec = vector.normalized_direction_vector()
-
-                for point in self.points:
-                    xi = point.x - first_point_not_nan.x
-                    yi = point.y - first_point_not_nan.y
-                    station_i = (norm_dir_vec[0] * xi +
-                                 norm_dir_vec[1] * yi)
-                    station.append(station_i)
-
-                z_min = self.z_min()
-                index_profile_z_min = list(
-                    filter(
-                        lambda z: z[1] == z_min,
-                        enumerate(self.z())
-                    )
-                )[0]
-                constant = station[index_profile_z_min[0]]
-
-            return list(map(lambda s: s - constant, station))
 
     def width_approximation(self):
         if self.has_standard_named_points():
@@ -477,58 +401,235 @@ class ProfileXYZ(Profile, SQLSubModel):
 
         return abs(rg.dist(rd))
 
-    def get_water_limits(self, z):
+    def wet_perimeter(self, z):
-        # ====================================================================
+        poly = self.wet_polygon(z)
-        #  détermination des points limites RG et RD pour un niveau
-        #  d'eau donné
-        #
-        #  irg et ird sont les premiers indices en partant des rives
-        #  gauche et droite qui correspondent à des points sous la
-        #  surface de l'eau ptX et ptY sont les points interpolés où
-        #  le plan d'eau intersecte le profil known_level est le
-        #  niveau d'eau pour lequel on a obtenu irg, ird, ptX et ptY
-        # ====================================================================
 
-        # initialisation
+        if poly is None:
-        irg = -1
+            return 0
-        ird = -1
+
+        return poly.length
+
+    def wet_area(self, z):
+        poly = self.wet_polygon(z)
+
+        if poly is None:
+            return 0
+
+        return poly.area
+
+    def wet_polygon(self, z):
+        points = self.wet_points(z)
+        if len(points) < 3:
+            return None
+
+        z = map(lambda p: p.z, points)
+        station = self._get_station(points)
+
+        poly = geometry.Polygon(list(zip(station, z)))
+        return poly
+
+    def wet_points(self, z):
+        left, right = self.get_water_limits(z)
+
+        points = list(filter(lambda p: p.z < z, self._points))
+        points = [left] + points + [right]
+        points = sorted(points, key=lambda p: p.x)
+
+        return points
+
+    def get_water_limits(self, z):
+        """
+        Determine left and right limits of water elevation.
+        """
+
+        # Get the index of first point with elevation lesser than water
+        # elevation (for the right and left river side)
+        i_left = -1
+        i_right = -1
 
         for i in range(self.number_points):
             if self.point(i).z <= z:
-                irg = i
+                i_left = i
+                break
 
         for i in reversed(range(self.number_points)):
             if self.point(i).z <= z:
-                ird = i
+                i_right = i
+                break
 
-        # interpolation des points ptX et ptY
+        # Interpolate points at river left side
-        if (irg < self.number_points - 1):
+        if (i_left > 0):
             x = np.interp(
                 z,
-                [self.point(irg).z, self.point(irg + 1).z],
+                [self.point(i_left).z, self.point(i_left - 1).z],
-                [self.point(irg).x, self.point(irg + 1).x]
+                [self.point(i_left).x, self.point(i_left - 1).x]
             )
             y = np.interp(
                 z,
-                [self.point(irg).z, self.point(irg + 1).z],
+                [self.point(i_left).z, self.point(i_left - 1).z],
-                [self.point(irg).y, self.point(irg + 1).y]
+                [self.point(i_left).y, self.point(i_left - 1).y]
             )
-            ptX = PointXYZ(x, y, z)
+            pt_left = PointXYZ(x, y, z, name="wl_left")
         else:
-            ptX = self.point(0)
+            pt_left = self.point(0)
-        if (ird > 0):
+
+        # Interpolate points at river right side
+        if (i_right < self.number_points - 1):
             x = np.interp(
                 z,
-                [self.point(ird-1).z, self.point(ird).z],
+                [self.point(i_right).z, self.point(i_right + 1).z],
-                [self.point(ird-1).x, self.point(ird).x]
+                [self.point(i_right).x, self.point(i_right + 1).x]
             )
             y = np.interp(
                 z,
-                [self.point(ird).z, self.point(ird - 1).z],
+                [self.point(i_right).z, self.point(i_right + 1).z],
-                [self.point(ird).y, self.point(ird - 1).y]
+                [self.point(i_right).y, self.point(i_right + 1).y]
             )
-            ptY = PointXYZ(x, y, z)
+            pt_right = PointXYZ(x, y, z, name="wl_right")
         else:
-            ptY = self.point(self.number_points - 1)
+            pt_right = self.point(self.number_points - 1)
 
-        return ptX, ptY
+        return pt_left, pt_right
+
+    def get_station(self):
+        """Projection of the points of the profile on a plane.
+
+        Args:
+            self: The profile
+
+        Returns:
+            Projection of the points of the profile on a plane.
+        """
+        if self.nb_points < 3:
+            return None
+        else:
+            return self._get_station(self.points)
+
+    @timer
+    def _get_station(self, points):
+        first_named_point = None
+        index_first_named_point = None
+        last_named_point = None
+
+        first_point_not_nan = self._first_point_not_nan(points)
+        last_point_not_nan = self._last_point_not_nan(points)
+
+        for index, point in enumerate(points):
+            if point.point_is_named():
+                index_first_named_point = index
+                first_named_point = point
+                break
+
+        for point in reversed(points):
+            if point.point_is_named():
+                last_named_point = point
+                break
+
+        station = []
+        constant = 0.0
+
+        if (first_named_point is not None
+                and last_named_point is not None):
+            if (first_named_point != last_named_point
+                    and first_named_point.x != last_named_point.x):
+                vector = Vector1d(first_named_point, last_named_point)
+                norm_dir_vec = vector.normalized_direction_vector()
+            else:
+                vector = Vector1d(first_point_not_nan, last_point_not_nan)
+                norm_dir_vec = vector.normalized_direction_vector()
+
+            for point in points:
+                xi = point.x - first_named_point.x
+                yi = point.y - first_named_point.y
+                station_i = (norm_dir_vec[0] * xi +
+                             norm_dir_vec[1] * yi)
+                station.append(station_i)
+
+            constant = station[index_first_named_point]
+        elif first_named_point is None:
+            vector = Vector1d(first_point_not_nan, last_point_not_nan)
+            norm_dir_vec = vector.normalized_direction_vector()
+
+            for point in points:
+                xi = point.x - first_point_not_nan.x
+                yi = point.y - first_point_not_nan.y
+                station_i = (norm_dir_vec[0] * xi +
+                             norm_dir_vec[1] * yi)
+                station.append(station_i)
+
+            z_min = self.z_min()
+            index_profile_z_min = next(
+                filter(
+                    lambda z: z[1] == z_min,
+                    enumerate(self.z())
+                )
+            )
+            constant = station[index_profile_z_min[0]]
+
+        return list(map(lambda s: s - constant, station))
+
+    def _first_point_not_nan(self, points):
+        first_point = None
+
+        for point in points:
+            if not point.is_nan():
+                first_point = point
+                break
+
+        return first_point
+
+    def _last_point_not_nan(self, points):
+        last_point = None
+
+        for point in reversed(points):
+            if not point.is_nan():
+                last_point = point
+                break
+
+        return last_point
+
+    def purge(self, np_purge):
+        """
+        Remove points to keep at most np_purge points.
+        """
+        if (self.nb_points <= np_purge):
+            return
+
+        nb_named = 2   # we consider the first and last point as named
+        area = [0.0]
+
+        for i in range(1, self.nb_points-1):
+            if self.point(i).point_is_named():
+                area.append(9999999.999)
+                nb_named += 1
+            else:
+                area.append(
+                    PointXYZ.areatriangle3d(
+                        self.point(i-1),
+                        self.point(i),
+                        self.point(i+1))
+                )
+
+        area.append(0.0)
+
+        while self.nb_points > max(np_purge, nb_named):
+            to_rm = np.argmin(area[1:self.nb_points - 1]) + 1
+
+            self.delete_i([to_rm])
+            area.pop(to_rm)
+
+            for i in [to_rm-1, to_rm]:
+                if (i == 0):
+                    continue
+
+                if (i == self.nb_points - 1):
+                    continue
+
+                if self.point(i).point_is_named():
+                    area[i] = 9999999.999
+                else:
+                    area[i] = PointXYZ.areatriangle3d(
+                        self.point(i-1),
+                        self.point(i),
+                        self.point(i+1)
+                    )

src/Model/Geometry/Reach.py

@@ -1,5 +1,5 @@
 # Reach.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -16,7 +16,9 @@
 
 # -*- coding: utf-8 -*-
 
+import os
 import logging
+import shapefile
 import numpy as np
 
 from time import time
@@ -65,7 +67,7 @@ class Reach(SQLSubModel):
 
         new._profiles = ProfileXYZ._db_load(
             execute,
-            data=data
+            data=data.copy()
         )
 
         return new
@@ -111,7 +113,7 @@ class Reach(SQLSubModel):
     def _get_profiles_list(self):
         # Profiles list generator is type (int, Point) with the first
         # element the index of the Point in list
-        logger.info(f"Load profiles from reach {self.name}")
+        logger.debug(f"Load profiles from reach {self.name}")
         return list(
             map(
                 lambda p: p[1],
@@ -139,10 +141,10 @@ class Reach(SQLSubModel):
     def profiles(self, profiles):
         self._profiles = profiles
 
-    def get_profiles_from_kp(self, kp):
+    def get_profiles_from_rk(self, rk):
         return list(
             filter(
-                lambda p: p.kp == kp, self.profiles
+                lambda p: p.rk == rk, self.profiles
             )
         )
 
@@ -333,18 +335,18 @@ class Reach(SQLSubModel):
             )
         )
 
-    def get_kp(self):
+    def get_rk(self):
-        """List of profiles kp
+        """List of profiles rk
 
         Returns:
-            List of profiles kp
+            List of profiles rk
         """
-        return [profile.kp for profile in self.profiles]
+        return [profile.rk for profile in self.profiles]
 
-    def get_kp_complete_profiles(self):
+    def get_rk_complete_profiles(self):
         return list(
             map(
-                lambda profile: profile.kp,
+                lambda profile: profile.rk,
                 filter(
                     lambda profile: len(profile) > 0,
                     self.profiles
@@ -352,18 +354,42 @@ class Reach(SQLSubModel):
             )
         )
 
-    def get_kp_min(self):
+    def get_rk_min(self):
-        if len(self.get_kp()) > 0:
+        if len(self.get_rk()) > 0:
-            return min(self.get_kp())
+            return min(self.get_rk())
         else:
             return 0.0
 
-    def get_kp_max(self):
+    def get_rk_max(self):
-        if len(self.get_kp()) > 0:
+        if len(self.get_rk()) > 0:
-            return max(self.get_kp())
+            return max(self.get_rk())
         else:
             return 0.0
 
+    def inter_profiles_rk(self):
+        profiles = sorted(self.profiles, key=lambda p: p.rk)
+        first = profiles[0]
+        last = profiles[-1]
+
+        res_rk = [first.rk]
+
+        profiles = iter(profiles)
+        previous = next(profiles)
+
+        for profile in profiles:
+            prev = previous.rk
+            curr = profile.rk
+
+            diff = abs(previous.rk - profile.rk)
+
+            new = previous.rk + (diff / 2.0)
+            res_rk.append(new)
+
+            previous = profile
+
+        res_rk.append(last.rk)
+        return res_rk
+
     # Sediment Layers
 
     def get_sl(self):
@@ -510,7 +536,7 @@ class Reach(SQLSubModel):
     def sort(self, is_reversed: bool = False):
         self.profiles = sorted(
             self.profiles,
-            key=lambda profile: profile.kp,
+            key=lambda profile: profile.rk,
             reverse=is_reversed
         )
         self._status.modified()
@@ -533,8 +559,66 @@ class Reach(SQLSubModel):
 
     # Import/Export
 
-    @timer
     def import_geometry(self, file_path_name: str):
+        ext = file_path_name.split(".")
+        if len(ext) > 0:
+            ext = ext[-1].lower()
+
+            if ext in ['st', 'm']:
+                return self.import_geometry_st(file_path_name)
+
+            if ext in ['shp']:
+                return self.import_geometry_shp(file_path_name)
+
+        raise FileFormatError(
+            file_path_name,
+            f"Geometry file extention ('.{ext}') unkown"
+        )
+
+    @timer
+    def import_geometry_shp(self, file_path_name: str):
+        sf = shapefile.Reader(
+            os.path.abspath(file_path_name)
+        )
+
+        if sf.shapeType != shapefile.POLYLINEZ:
+            raise FileFormatError(
+                file_path_name,
+                "Shapefile is not a POLYLINEZ"
+            )
+
+        profiles = []
+
+        for i in range(len(sf)):
+            s_profile = sf.shape(i)
+            z = s_profile.z
+
+            ind = 0
+            points = []
+            for point in s_profile.points:
+                points.append([
+                    point[0],
+                    point[1],
+                    z[ind]
+                ])
+
+                ind += 1
+
+            prof = ProfileXYZ(
+                reach=self, status=self._status
+            )
+            prof.import_points(points)
+
+            profiles.append(prof)
+
+        self.profiles = profiles + self.profiles
+        self._update_profile_numbers()
+        self._recompute_rk()
+
+        return profiles
+
+    @timer
+    def import_geometry_st(self, file_path_name: str):
         """Import a geometry from file (.ST or .st)
 
         Args:
@@ -549,7 +633,7 @@ class Reach(SQLSubModel):
         try:
             list_profile, list_header = self.read_file_st(str(file_path_name))
             profile_header = ["num", "code1",
-                              "code2", "nb_point", "kp", "name"]
+                              "code2", "nb_point", "rk", "name"]
 
             if list_profile and list_header:
                 for ind, profile in enumerate(list_profile):
@@ -637,12 +721,12 @@ class Reach(SQLSubModel):
                 c1 = f"{profile.code1:>6}"
                 c2 = f"{profile.code2:>6}"
                 t = f"{len(profile.points):>6}"
-                kp = f"{profile.kp:>12f}"[0:12]
+                rk = f"{profile.rk:>12f}"[0:12]
                 pname = profile.name
                 if profile.name == "":
                     pname = f"p{profile.id:>3}".replace(" ", "0")
 
-                st.write(f"{num}{c1}{c2}{t} {kp} {pname}\n")
+                st.write(f"{num}{c1}{c2}{t} {rk} {pname}\n")
 
                 for point in profile.points:
                     x = f"{point.x:<12.4f}"[0:12]
@@ -661,15 +745,15 @@ class Reach(SQLSubModel):
         last = self.profile(len(self) - 1)
 
         z_first = first.z_min()
-        kp_first = first.kp
+        rk_first = first.rk
 
         z_last = last.z_min()
-        kp_last = last.kp
+        rk_last = last.rk
 
         return (
             (z_last - z_first)
             /
-            (kp_last - kp_first)
+            (rk_last - rk_first)
         )
 
     def get_incline_mean(self):
@@ -680,15 +764,15 @@ class Reach(SQLSubModel):
 
         for profile in profiles[1:]:
             z_first = previous.z_min()
-            kp_first = previous.kp
+            rk_first = previous.rk
 
             z_last = profile.z_min()
-            kp_last = profile.kp
+            rk_last = profile.rk
 
             incline_acc += (
                 (z_last - z_first)
                 /
-                (kp_last - kp_first)
+                (rk_last - rk_first)
             )
 
             previous = profile
@@ -703,15 +787,15 @@ class Reach(SQLSubModel):
 
         for profile in profiles[1:]:
             z_first = previous.z_min()
-            kp_first = previous.kp
+            rk_first = previous.rk
 
             z_last = profile.z_min()
-            kp_last = profile.kp
+            rk_last = profile.rk
 
             incline_acc += [
                 (z_last - z_first)
                 /
-                (kp_last - kp_first)
+                (rk_last - rk_first)
             ]
 
             previous = profile
@@ -727,15 +811,15 @@ class Reach(SQLSubModel):
 
         for profile in profiles[1:]:
             z_first = previous.z_min()
-            kp_first = previous.kp
+            rk_first = previous.rk
 
             z_last = profile.z_min()
-            kp_last = profile.kp
+            rk_last = profile.rk
 
             incline_acc += [
                 (z_last - z_first)
                 /
-                (kp_last - kp_first)
+                (rk_last - rk_first)
             ]
 
             previous = profile
@@ -743,7 +827,10 @@ class Reach(SQLSubModel):
         incline_acc.sort()
 
         marge = round(len(incline_acc) * 0.1)
-        incline_set = incline_acc[marge:-marge]
+        if marge > 0:
+            incline_set = incline_acc[marge:-marge]
+        else:
+            incline_set = incline_acc
 
         logger.debug(f"+{incline_acc}")
         logger.debug(f"-{incline_set}")
@@ -759,3 +846,24 @@ class Reach(SQLSubModel):
         except Exception as e:
             logger_exception(e)
             return 0
+
+    def _recompute_rk(self, offset=0.0):
+        self._recompute_rk_no_gl(offset=offset)
+
+    def _recompute_rk_no_gl(self, offset=0.0):
+        profiles = iter(self.profiles)
+
+        previous = next(profiles)
+        previous.rk = offset
+
+        for profile in profiles:
+            prev_points = previous.points
+            curr_points = profile.points
+
+            dist = (
+                prev_points[0].dist_2d(curr_points[0]) +
+                prev_points[-1].dist_2d(curr_points[-1])
+            ) / 2.0
+
+            profile.rk = previous.rk + dist
+            previous = profile

src/Model/Geometry/Vector_1d.py

@@ -1,5 +1,5 @@
 # Vector_1d.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/HydraulicStructures/Basic/HydraulicStructures.py

@@ -1,5 +1,5 @@
 # HydraulicStructures.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -158,6 +158,9 @@ class BasicHS(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"{self._type}{self.id + 1}"
+
         return self._name
 
     @name.setter

src/Model/HydraulicStructures/Basic/Types.py

@@ -1,5 +1,5 @@
 # Types.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/HydraulicStructures/Basic/Value.py

@@ -1,5 +1,5 @@
 # Value.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/HydraulicStructures/HydraulicStructures.py

@@ -1,5 +1,5 @@
 # HydraulicStructures.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -50,8 +50,8 @@ class HydraulicStructure(SQLSubModel):
             self.id = id
 
         self._name = name
-        self._input_kp = None
+        self._input_rk = None
-        self._output_kp = None
+        self._output_rk = None
         self._input_reach = None
         self._output_reach = None
         self._enabled = True
@@ -69,8 +69,8 @@ class HydraulicStructure(SQLSubModel):
             id INTEGER NOT NULL PRIMARY KEY,
             name TEXT NOT NULL,
             enabled BOOLEAN NOT NULL,
-            input_kp REAL NOT NULL,
+            input_rk REAL NOT NULL,
-            output_kp REAL NOT NULL,
+            output_rk REAL NOT NULL,
             input_reach INTEGER,
             output_reach INTEGER,
             FOREIGN KEY(input_reach) REFERENCES river_reach(id),
@@ -84,9 +84,25 @@ class HydraulicStructure(SQLSubModel):
     def _db_update(cls, execute, version):
         major, minor, release = version.strip().split(".")
         if major == minor == "0":
-            if int(release) < 6:
+            rl = int(release)
+
+            if rl < 6:
                 cls._db_create(execute)
 
+            if rl < 11:
+                execute(
+                    """
+                    ALTER TABLE hydraulic_structures
+                    RENAME COLUMN input_kp TO input_rk
+                    """
+                )
+                execute(
+                    """
+                    ALTER TABLE hydraulic_structures
+                    RENAME COLUMN output_kp TO output_rk
+                    """
+                )
+
         return True
 
     @classmethod
@@ -95,7 +111,7 @@ class HydraulicStructure(SQLSubModel):
 
         table = execute(
             "SELECT id, name, enabled, " +
-            "input_kp, output_kp, " +
+            "input_rk, output_rk, " +
             "input_reach, output_reach " +
             "FROM hydraulic_structures "
         )
@@ -106,8 +122,8 @@ class HydraulicStructure(SQLSubModel):
             hs_id = next(it)
             name = next(it)
             enabled = (next(it) == 1)
-            input_kp = next(it)
+            input_rk = next(it)
-            output_kp = next(it)
+            output_rk = next(it)
             input_reach_id = next(it)
             output_reach_id = next(it)
 
@@ -118,8 +134,8 @@ class HydraulicStructure(SQLSubModel):
             )
 
             hs.enabled = enabled
-            hs.input_kp = input_kp if input_kp != -1 else None
+            hs.input_rk = input_rk if input_rk != -1 else None
-            hs.output_kp = output_kp if output_kp != -1 else None
+            hs.output_rk = output_rk if output_rk != -1 else None
 
             hs.input_reach, hs.output_reach = reduce(
                 lambda acc, n: (
@@ -148,24 +164,24 @@ class HydraulicStructure(SQLSubModel):
         if self._output_reach is not None:
             output_reach_id = self._output_reach.id
 
-        input_kp = -1
+        input_rk = -1
-        if self.input_kp is not None:
+        if self.input_rk is not None:
-            input_kp = self.input_kp
+            input_rk = self.input_rk
 
-        output_kp = -1
+        output_rk = -1
-        if self.output_kp is not None:
+        if self.output_rk is not None:
-            output_kp = self.output_kp
+            output_rk = self.output_rk
 
         sql = (
             "INSERT INTO " +
             "hydraulic_structures(" +
-            "  id, name, enabled, input_kp, output_kp, " +
+            "  id, name, enabled, input_rk, output_rk, " +
             "  input_reach, output_reach" +
             ") " +
             "VALUES (" +
             f"{self.id}, '{self._db_format(self._name)}', " +
             f"{self._db_format(self.enabled)}, " +
-            f"{input_kp}, {output_kp}, " +
+            f"{input_rk}, {output_rk}, " +
             f"{input_reach_id}, {output_reach_id}" +
             ")"
         )
@@ -187,6 +203,9 @@ class HydraulicStructure(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"HS{self.id + 1}"
+
         return self._name
 
     @name.setter
@@ -195,24 +214,24 @@ class HydraulicStructure(SQLSubModel):
         self._status.modified()
 
     @property
-    def input_kp(self):
+    def input_rk(self):
-        return self._input_kp
+        return self._input_rk
 
-    @input_kp.setter
+    @input_rk.setter
-    def input_kp(self, input_kp):
+    def input_rk(self, input_rk):
-        if input_kp is not None:
+        if input_rk is not None:
-            input_kp = float(input_kp)
+            input_rk = float(input_rk)
 
-        self._input_kp = input_kp
+        self._input_rk = input_rk
         self._status.modified()
 
     @property
-    def output_kp(self):
+    def output_rk(self):
-        return self._output_kp
+        return self._output_rk
 
-    @output_kp.setter
+    @output_rk.setter
-    def output_kp(self, output_kp):
+    def output_rk(self, output_rk):
-        self._output_kp = output_kp
+        self._output_rk = output_rk
         self._status.modified()
 
     @property

src/Model/HydraulicStructures/HydraulicStructuresList.py

@@ -1,5 +1,5 @@
 # HydraulicStructuresList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/InitialConditions/InitialConditions.py

@@ -1,5 +1,5 @@
 # InitialConditions.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -30,7 +30,7 @@ logger = logging.getLogger()
 class Data(SQLSubModel):
     def __init__(self, name: str = "",
                  comment: str = "", reach=None,
-                 kp: float = 0.0, discharge: float = 0.0,
+                 rk: float = 0.0, discharge: float = 0.0,
                  height: float = 0.0,
                  status=None):
         super(Data, self).__init__()
@@ -42,14 +42,14 @@ class Data(SQLSubModel):
         self._name = name
         self._comment = comment
 
-        self._kp = kp
+        self._rk = rk
         self._discharge = discharge
         self._speed = 0.0
         self._elevation = 0.0
         self._height = height
 
-        if self._kp != 0.0:
+        if self._rk != 0.0:
-            self._update_from_kp()
+            self._update_from_rk()
         if self._height != 0.0:
             self._update_from_height()
         if self._discharge != 0.0:
@@ -64,7 +64,7 @@ class Data(SQLSubModel):
             name TEXT NOT NULL,
             comment TEXT NOT NULL,
             reach INTEGER,
-            kp REAL NOT NULL,
+            rk REAL NOT NULL,
             discharge REAL NOT NULL,
             height REAL NOT NULL,
             FOREIGN KEY(reach) REFERENCES river_reach(id)
@@ -75,13 +75,20 @@ class Data(SQLSubModel):
 
     @classmethod
     def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 11:
+                execute(
+                    "ALTER TABLE initial_conditions RENAME COLUMN kp TO rk"
+                )
+
         return cls._update_submodel(execute, version)
 
     @classmethod
     def _db_load(cls, execute, data=None):
         id = data["reach"].id
         table = execute(
-            "SELECT ind, name, comment, kp, discharge, height " +
+            "SELECT ind, name, comment, rk, discharge, height " +
             "FROM initial_conditions " +
             f"WHERE reach = {id}"
         )
@@ -95,7 +102,7 @@ class Data(SQLSubModel):
             ind = row[0]
             name = row[1]
             comment = row[2]
-            kp = row[3]
+            rk = row[3]
             discharge = row[4]
             height = row[5]
 
@@ -104,7 +111,7 @@ class Data(SQLSubModel):
                 status=data["status"],
                 name=name,
                 comment=comment,
-                kp=kp,
+                rk=rk,
                 discharge=discharge,
                 height=height,
             )
@@ -118,12 +125,12 @@ class Data(SQLSubModel):
 
         execute(
             "INSERT INTO " +
-            "initial_conditions(ind, name, comment, kp, " +
+            "initial_conditions(ind, name, comment, rk, " +
             "discharge, height, reach) " +
             "VALUES (" +
             f"{ind}, '{self._db_format(self.name)}', " +
             f"'{self._db_format(self._comment)}', " +
-            f"{self._kp}, {self._discharge}, {self._height}, " +
+            f"{self._rk}, {self._discharge}, {self._height}, " +
             f"{self._reach.id}" +
             ")"
         )
@@ -134,7 +141,7 @@ class Data(SQLSubModel):
         new = Data(
             name=self.name,
             comment=self._comment,
-            kp=self._kp,
+            rk=self._rk,
             discharge=self._discharge,
             height=self._height,
             reach=self._reach,
@@ -154,8 +161,8 @@ class Data(SQLSubModel):
             val = self._name
         elif key == "comment":
             val = self._comment
-        elif key == "kp":
+        elif key == "rk":
-            val = self._kp
+            val = self._rk
         elif key == "speed":
             val = self._speed
         elif key == "discharge":
@@ -168,7 +175,7 @@ class Data(SQLSubModel):
         return val
 
     def _update_get_min(self):
-        profile = self._reach.reach.get_profiles_from_kp(self._kp)
+        profile = self._reach.reach.get_profiles_from_rk(self._rk)
         if len(profile) > 0:
             min = profile[0].z_min()
         else:
@@ -176,7 +183,7 @@ class Data(SQLSubModel):
 
         return min
 
-    def _update_from_kp(self):
+    def _update_from_rk(self):
         min = self._update_get_min()
         self._elevation = min + self._height
 
@@ -197,9 +204,9 @@ class Data(SQLSubModel):
             self._name = str(value)
         elif key == "comment":
             self._comment = str(value)
-        elif key == "kp":
+        elif key == "rk":
-            self._kp = float(value)
+            self._rk = float(value)
-            self._update_from_kp()
+            self._update_from_rk()
         elif key == "speed":
             # Not supposed to be modified
             self._speed = float(value)
@@ -266,6 +273,9 @@ class InitialConditions(SQLSubModel):
     def __len__(self):
         return len(self._data)
 
+    def lst(self):
+        return self._data
+
     @property
     def reach(self):
         return self._reach
@@ -295,6 +305,15 @@ class InitialConditions(SQLSubModel):
         self._data.insert(index, n)
         self._status.modified()
 
+    def new_from_data(self, rk, discharge, elevation):
+        n = Data(reach=self._reach, status=self._status)
+
+        n['rk'] = rk
+        n['discharge'] = discharge
+        n['elevation'] = elevation
+
+        return n
+
     def insert(self, index, data):
         self._data.insert(index, data)
         self._status.modified()
@@ -332,8 +351,8 @@ class InitialConditions(SQLSubModel):
             )
         )
 
-    def get_kp(self):
+    def get_rk(self):
-        return self._data_get("kp")
+        return self._data_get("rk")
 
     def get_elevation(self):
         return self._data_get("elevation")
@@ -341,10 +360,10 @@ class InitialConditions(SQLSubModel):
     def get_discharge(self):
         return self._data_get("discharge")
 
-    def _sort_by_z_and_kp(self, profiles):
+    def _sort_by_z_and_rk(self, profiles):
         profiles.sort(
             reverse=False,
-            key=lambda p: p.kp
+            key=lambda p: p.rk
         )
 
         first_z = profiles[0].z()
@@ -353,14 +372,14 @@ class InitialConditions(SQLSubModel):
         if first_z > last_z:
             profiles.sort(
                 reverse=True,
-                key=lambda p: p.kp
+                key=lambda p: p.rk
             )
 
     def generate_growing_constante_height(self, height: float):
         self._data = []
 
         profiles = self._reach.reach.profiles.copy()
-        self._sort_by_z_and_kp(profiles)
+        self._sort_by_z_and_rk(profiles)
 
         incline = self._reach.reach.get_incline_median_mean()
         logger.debug(f"incline = {incline}")
@@ -381,13 +400,13 @@ class InitialConditions(SQLSubModel):
                 previous_elevation
             )
 
-            logger.debug(f"({profile.kp}):")
+            logger.debug(f"({profile.rk}):")
             logger.debug(f"  width  = {width}")
             logger.debug(f"  strickler = {strickler}")
             logger.debug(f"  discharge = {discharge}")
 
             new = Data(reach=self._reach, status=self._status)
-            new["kp"] = profile.kp
+            new["rk"] = profile.rk
             new["discharge"] = discharge
 
             new["elevation"] = elevation
@@ -406,7 +425,7 @@ class InitialConditions(SQLSubModel):
 
     def _generate_height_estimation_from_discharge(self, discharge: float):
         profiles = self._reach.reach.profiles.copy()
-        self._sort_by_z_and_kp(profiles)
+        self._sort_by_z_and_rk(profiles)
 
         previous_elevation = -99999.99
 
@@ -427,13 +446,13 @@ class InitialConditions(SQLSubModel):
                 previous_elevation
             )
 
-            logger.debug(f"({profile.kp}):")
+            logger.debug(f"({profile.rk}):")
             logger.debug(f"  width  = {width}")
             logger.debug(f"  strickler = {strickler}")
-            logger.debug(f"  hieght = {height}")
+            logger.debug(f"  height = {height}")
 
             new = Data(reach=self._reach, status=self._status)
-            new["kp"] = profile.kp
+            new["rk"] = profile.rk
             new["discharge"] = discharge
             new["elevation"] = elevation
 
@@ -444,10 +463,10 @@ class InitialConditions(SQLSubModel):
 
     def _generate_resort_data(self, profiles):
         is_reverse = False
-        if profiles[0].kp > profiles[-1].kp:
+        if profiles[0].rk > profiles[-1].rk:
             is_reverse = True
 
         self._data.sort(
             reverse=not is_reverse,
-            key=lambda d: d['kp']
+            key=lambda d: d['rk']
         )

src/Model/InitialConditions/InitialConditionsDict.py

@@ -1,5 +1,5 @@
 # InitialConditionsDict.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/LateralContribution/LateralContribution.py

@@ -1,5 +1,5 @@
 # LateralContribution.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -18,7 +18,12 @@
 
 import logging
 
-from tools import trace, timer, old_pamhyr_date_to_timestamp
+from tools import (
+    trace, timer,
+    old_pamhyr_date_to_timestamp,
+    date_iso_to_timestamp,
+    date_dmy_to_timestamp,
+)
 
 from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import NotImplementedMethodeError
@@ -43,8 +48,8 @@ class LateralContribution(SQLSubModel):
         self._name = name
         self._type = ""
         self._edge = None
-        self._begin_kp = 0.0
+        self._begin_rk = 0.0
-        self._end_kp = 0.0
+        self._end_rk = 0.0
         self._data = []
         self._header = []
         self._types = [float, float]
@@ -61,8 +66,8 @@ class LateralContribution(SQLSubModel):
             type TEXT NOT NULL,
             tab TEXT NOT NULL,
             edge INTEGER,
-            begin_kp REAL NOT NULL,
+            begin_rk REAL NOT NULL,
-            end_kp REAL NOT NULL,
+            end_rk REAL NOT NULL,
             FOREIGN KEY(edge) REFERENCES river_reach(id)
           )
         """)
@@ -82,6 +87,22 @@ class LateralContribution(SQLSubModel):
 
     @classmethod
     def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 11:
+                execute(
+                    """
+                    ALTER TABLE lateral_contribution
+                    RENAME COLUMN begin_kp TO begin_rk
+                    """
+                )
+                execute(
+                    """
+                    ALTER TABLE lateral_contribution
+                    RENAME COLUMN end_kp TO end_rk
+                    """
+                )
+
         return True
 
     @classmethod
@@ -105,7 +126,7 @@ class LateralContribution(SQLSubModel):
         tab = data["tab"]
 
         table = execute(
-            "SELECT id, name, type, edge, begin_kp, end_kp " +
+            "SELECT id, name, type, edge, begin_rk, end_rk " +
             f"FROM lateral_contribution WHERE tab = '{tab}'"
         )
 
@@ -120,8 +141,8 @@ class LateralContribution(SQLSubModel):
             lc.edge = None
             if row[3] != -1:
                 lc.edge = next(filter(lambda e: e.id == row[3], data["edges"]))
-            lc._begin_kp = row[4]
+            lc._begin_rk = row[4]
-            lc._end_kp = row[5]
+            lc._end_rk = row[5]
 
             values = execute(
                 "SELECT ind, data0, data1 FROM lateral_contribution_data " +
@@ -155,11 +176,11 @@ class LateralContribution(SQLSubModel):
         sql = (
             "INSERT INTO " +
             "lateral_contribution(id, name, type, tab, " +
-            "edge, begin_kp, end_kp) " +
+            "edge, begin_rk, end_rk) " +
             "VALUES (" +
             f"{self.id}, '{self._db_format(self._name)}', " +
             f"'{self._db_format(self._type)}', '{tab}', {edge}, " +
-            f"{self._begin_kp}, {self._end_kp}" +
+            f"{self._begin_rk}, {self._end_rk}" +
             ")"
         )
         execute(sql)
@@ -189,6 +210,10 @@ class LateralContribution(SQLSubModel):
     @classmethod
     def time_convert(cls, data):
         if type(data) is str:
+            if data.count("-") == 2:
+                return date_iso_to_timestamp(data)
+            if data.count("/") == 2:
+                return date_dmy_to_timestamp(data)
             if data.count(":") == 3:
                 return old_pamhyr_date_to_timestamp(data)
             if data.count(":") == 2:
@@ -200,6 +225,9 @@ class LateralContribution(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"L{self.id + 1}"
+
         return self._name
 
     @name.setter
@@ -219,44 +247,44 @@ class LateralContribution(SQLSubModel):
     def edge(self, edge):
         self._edge = edge
         if edge is not None:
-            self._begin_kp = self._edge.reach.get_kp_min()
+            self._begin_rk = self._edge.reach.get_rk_min()
-            self._end_kp = self._edge.reach.get_kp_max()
+            self._end_rk = self._edge.reach.get_rk_max()
         self._status.modified()
 
     def has_edge(self):
         return self._edge is not None
 
     @property
-    def begin_kp(self):
+    def begin_rk(self):
-        return self._begin_kp
+        return self._begin_rk
 
-    @begin_kp.setter
+    @begin_rk.setter
-    def begin_kp(self, begin_kp):
+    def begin_rk(self, begin_rk):
         if self._edge is None:
-            self._begin_kp = begin_kp
+            self._begin_rk = begin_rk
         else:
-            _min = self._edge.reach.get_kp_min()
+            _min = self._edge.reach.get_rk_min()
-            _max = self._edge.reach.get_kp_max()
+            _max = self._edge.reach.get_rk_max()
 
-            if _min <= begin_kp <= _max:
+            if _min <= begin_rk <= _max:
-                self._begin_kp = begin_kp
+                self._begin_rk = begin_rk
 
         self._status.modified()
 
     @property
-    def end_kp(self):
+    def end_rk(self):
-        return self._end_kp
+        return self._end_rk
 
-    @end_kp.setter
+    @end_rk.setter
-    def end_kp(self, end_kp):
+    def end_rk(self, end_rk):
         if self._edge is None:
-            self._end_kp = end_kp
+            self._end_rk = end_rk
         else:
-            _min = self._edge.reach.get_kp_min()
+            _min = self._edge.reach.get_rk_min()
-            _max = self._edge.reach.get_kp_max()
+            _max = self._edge.reach.get_rk_max()
 
-            if _min <= end_kp <= _max:
+            if _min <= end_rk <= _max:
-                self._end_kp = end_kp
+                self._end_rk = end_rk
 
         self._status.modified()
 
@@ -365,8 +393,8 @@ class LateralContribution(SQLSubModel):
     def convert(self, cls):
         new = cls(name=self.name, status=self._status)
         new.edge = self.edge
-        new.begin_kp = self.begin_kp
+        new.begin_rk = self.begin_rk
-        new.end_kp = self.end_kp
+        new.end_rk = self.end_rk
 
         for i, _ in enumerate(self.data):
             new.add(i)

src/Model/LateralContribution/LateralContributionList.py

@@ -1,5 +1,5 @@
 # LateralContributionList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/LateralContribution/LateralContributionTypes.py

@@ -1,5 +1,5 @@
 # LateralContributionTypes.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Network/Edge.py

@@ -1,5 +1,5 @@
 # Edge.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Network/Graph.py

@@ -1,5 +1,5 @@
 # Graph.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -67,6 +67,13 @@ class Graph(object):
     def edges_counts(self):
         return len(self._edges)
 
+    def enable_nodes_counts(self):
+        return reduce(
+            lambda acc, n: acc + 1 if self.is_enable_node(n) else acc,
+            self._nodes,
+            0
+        )
+
     def enable_edges_counts(self):
         return reduce(
             lambda acc, e: acc + 1 if e.is_enable() else acc,
@@ -135,26 +142,21 @@ class Graph(object):
     def insert_node(self, node):
         return self._add_node(node)
 
-    def remove_node(self, node_name: str):
+    def remove_node(self, node):
-        self._nodes = list(
+        self._nodes.remove(node)
-            filter(
+        self._remove_associated_edge(node)
-                lambda n: n.name != node_name,
-                self._nodes
-            )
-        )
-        self._remove_associated_edge(node_name)
         self._status.modified()
 
-    def _remove_associated_edge(self, node_name: str):
+    def _remove_associated_edge(self, node: str):
         edges = list(
             filter(
-                lambda e: (e.node1.name == node_name or
+                lambda e: (e.node1 == node or
-                           e.node2.name == node_name),
+                           e.node2 == node),
                 self._edges,
             )
         )
         for edge in edges:
-            self.remove_edge(edge.name)
+            self.remove_edge(edge)
 
     def create_node(self, x: float = 0.0, y: float = 0.0):
         node = self._create_node(x, y)
@@ -169,11 +171,11 @@ class Graph(object):
         return edge
 
     def _add_edge(self, edge):
-        # This edge already exists ?
+        # # This edge already exists ?
-        if any(filter(lambda e: (e.node1 == edge.node1 and
+        # if any(filter(lambda e: (e.node1 == edge.node1 and
-                                 e.node2 == edge.node2),
+        #                          e.node2 == edge.node2),
-                      self._edges)):
+        #               self._edges)):
-            return None
+        #     return None
 
         self._edges.append(edge)
 
@@ -190,13 +192,8 @@ class Graph(object):
     def create_edge(self, n1: Node, n2: Node):
         return self._create_edge(n1, n2)
 
-    def remove_edge(self, edge_name: str):
+    def remove_edge(self, edge):
-        self._edges = list(
+        self._edges.remove(edge)
-            filter(
-                lambda e: e.name != edge_name,
-                self._edges
-            )
-        )
         self._status.modified()
 
     def is_upstream_node(self, node):
@@ -213,6 +210,12 @@ class Graph(object):
             True
         )
 
+    def is_internal_node(self, node):
+        return not (
+            self.is_upstream_node(node) or
+            self.is_downstream_node(node)
+        )
+
     def is_enable_node(self, node):
         return reduce(
             lambda acc, e: (

src/Model/Network/Node.py

@@ -1,5 +1,5 @@
 # Node.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Network/Point.py

@@ -1,5 +1,5 @@
 # Point.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Network/__init__.py

@@ -1,5 +1,5 @@
 # __init__.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Network/test_network.py

@@ -1,5 +1,5 @@
 # test_Network.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -60,7 +60,7 @@ class GraphTestCase(unittest.TestCase):
 
         e0 = g.add_edge(n0, n1)
 
-        g.remove_edge(e0.name)
+        g.remove_edge(e0)
 
         self.assertEqual(g.nodes_counts(), 2)
         self.assertEqual(g.edges_counts(), 0)
@@ -73,7 +73,7 @@ class GraphTestCase(unittest.TestCase):
 
         e0 = g.add_edge(n0, n1)
 
-        g.remove_node(n0.name)
+        g.remove_node(n0)
 
         self.assertEqual(g.nodes_counts(), 1)
         self.assertEqual(g.edges_counts(), 0)
@@ -88,7 +88,7 @@ class GraphTestCase(unittest.TestCase):
         e0 = g.add_edge(n0, n1)
         e1 = g.add_edge(n1, n2)
 
-        g.remove_node(n1.name)
+        g.remove_node(n1)
 
         self.assertEqual(g.nodes_counts(), 2)
         self.assertEqual(g.edges_counts(), 0)

src/Model/REPLine/REPLine.py

@@ -0,0 +1,180 @@
+# REPLine.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+from functools import reduce
+
+from tools import trace, timer
+
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Except import NotImplementedMethodeError
+
+
+class REPLine(SQLSubModel):
+    _sub_classes = []
+    _id_cnt = 0
+
+    def __init__(self, id: int = -1, enabled=True,
+                 name="", line="", solvers=set(),
+                 status=None):
+        super(REPLine, self).__init__()
+
+        if id == -1:
+            self.id = REPLine._id_cnt
+        else:
+            self.id = id
+
+        self._status = status
+
+        self._enabled = enabled
+        self._name = f"Line{self.id}" if name == "" else name
+        self._line = line
+        self._solvers = solvers
+
+        REPLine._id_cnt = max(id, REPLine._id_cnt+1)
+
+    def __getitem__(self, key):
+        value = None
+
+        if key == "enabled":
+            value = self._enabled
+        elif key == "name":
+            value = self._name
+        elif key == "line":
+            value = self._line
+        elif key == "solvers":
+            value = self._solvers
+
+        return value
+
+    def __setitem__(self, key, value):
+        if key == "enabled":
+            self._enabled = value
+        elif key == "name":
+            self._name = value
+        elif key == "line":
+            self._line = value
+        elif key == "solvers":
+            self._solvers = value
+
+        self._status.modified()
+
+    @property
+    def enabled(self):
+        return self._enabled
+
+    @enabled.setter
+    def enabled(self, enabled):
+        self._enabled = enabled
+        self._status.modified()
+
+    def is_enabled(self):
+        return self._enabled
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+        self._status.modified()
+
+    @property
+    def line(self):
+        return self._line
+
+    @line.setter
+    def line(self, line):
+        self._line = line
+        self._status.modified()
+
+    @property
+    def solvers(self):
+        return self._solvers
+
+    @solvers.setter
+    def solvers(self, solvers):
+        self._solvers = solvers
+        self._status.modified()
+
+    @classmethod
+    def _db_create(cls, execute):
+        execute("""
+          CREATE TABLE rep_lines(
+            id INTEGER NOT NULL PRIMARY KEY,
+            enabled BOOLEAN NOT NULL,
+            name TEXT NOT NULL,
+            line TEXT NOT NULL,
+            solvers TEXT NOT NULL
+          )
+        """)
+
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 9:
+                cls._db_create(execute)
+
+        return True
+
+    @classmethod
+    def _db_load(cls, execute, data=None):
+        new = []
+
+        table = execute(
+            "SELECT id, enabled, name, line, solvers " +
+            "FROM rep_lines"
+        )
+
+        for row in table:
+            it = iter(row)
+
+            id = next(it)
+            enabled = (next(it) == 1)
+            name = next(it)
+            line = next(it)
+            solvers = set(next(it).split(";;"))
+
+            f = cls(
+                id=id, enabled=enabled, name=name, line=line,
+                solvers=solvers, status=data['status']
+            )
+
+            new.append(f)
+
+        return new
+
+    def _db_save(self, execute, data=None):
+        solvers = ";;".join(self._solvers)
+
+        sql = (
+            "INSERT INTO " +
+            "rep_lines(id, enabled, name, line, solvers) " +
+            "VALUES (" +
+            f"{self.id}, {self._enabled}, " +
+            f"'{self._db_format(self._name)}', " +
+            f"'{self._db_format(self._line)}', " +
+            f"'{self._db_format(solvers)}'" +
+            ")"
+        )
+        execute(sql)
+
+        return True

src/Model/REPLine/REPLineList.py

@@ -0,0 +1,56 @@
+# REPLineList.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+from tools import trace, timer
+
+from Model.Except import NotImplementedMethodeError
+from Model.Tools.PamhyrList import PamhyrModelList
+from Model.REPLine.REPLine import REPLine
+
+
+class REPLineList(PamhyrModelList):
+    _sub_classes = [REPLine]
+
+    @classmethod
+    def _db_load(cls, execute, data=None):
+        new = cls(status=data["status"])
+
+        new._lst = REPLine._db_load(execute, data)
+
+        return new
+
+    def _db_save(self, execute, data=None):
+        ok = True
+
+        # Delete previous data
+        execute("DELETE FROM rep_lines")
+
+        for af in self._lst:
+            ok &= af._db_save(execute, data)
+
+        return ok
+
+    @property
+    def lines(self):
+        return self.lst
+
+    def new(self, index):
+        n = REPLine(status=self._status)
+        self.insert(index, n)
+        self._status.modified()
+        return n

src/Model/Reservoir/Reservoir.py

@@ -1,5 +1,5 @@
 # Reservoir.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -152,6 +152,9 @@ class Reservoir(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"R{self.id + 1}"
+
         return self._name
 
     @name.setter

src/Model/Reservoir/ReservoirList.py

@@ -1,5 +1,5 @@
 # ReservoirList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Results/Results.py

@@ -1,5 +1,5 @@
 # Results.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Results/River/River.py

@@ -1,5 +1,5 @@
 # River.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -35,8 +35,8 @@ class Profile(object):
         return self._profile.name
 
     @property
-    def kp(self):
+    def rk(self):
-        return self._profile.kp
+        return self._profile.rk
 
     @property
     def geometry(self):
@@ -59,6 +59,9 @@ class Profile(object):
     def get_ts_key(self, timestamp, key):
         return self._data[timestamp][key]
 
+    def has_sediment(self):
+        return any(map(lambda ts: "sl" in self._data[ts], self._data))
+
 
 class Reach(object):
     def __init__(self, reach, study):
@@ -92,6 +95,9 @@ class Reach(object):
     def set(self, profile_id, timestamp, key, data):
         self._profiles[profile_id].set(timestamp, key, data)
 
+    def has_sediment(self):
+        return any(map(lambda profile: profile.has_sediment(), self._profiles))
+
 
 class River(object):
     def __init__(self, study):
@@ -120,3 +126,11 @@ class River(object):
 
         self._reachs.append(new)
         return new
+
+    def get_reach_by_geometry(self, geometry_reach):
+        return next(
+            filter(
+                lambda r: r.geometry is geometry_reach,
+                self._reachs
+            )
+        )

src/Model/River.py

@@ -1,5 +1,5 @@
 # River.py -- Pamhyr river model
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -40,6 +40,8 @@ from Model.Reservoir.ReservoirList import ReservoirList
 from Model.HydraulicStructures.HydraulicStructuresList import (
     HydraulicStructureList,
 )
+from Model.AdditionalFile.AddFileList import AddFileList
+from Model.REPLine.REPLineList import REPLineList
 
 from Solver.Solvers import solver_type_list
 
@@ -224,6 +226,8 @@ class River(Graph, SQLSubModel):
         SedimentLayerList,
         ReservoirList,
         HydraulicStructureList,
+        AddFileList,
+        REPLineList,
     ]
 
     def __init__(self, status=None):
@@ -245,6 +249,8 @@ class River(Graph, SQLSubModel):
         self._hydraulic_structures = HydraulicStructureList(
             status=self._status
         )
+        self._additional_files = AddFileList(status=self._status)
+        self._rep_lines = REPLineList(status=self._status)
 
     @classmethod
     def _db_create(cls, execute):
@@ -263,66 +269,62 @@ class River(Graph, SQLSubModel):
         # Stricklers (Stricklers is load in first because it's needed
         # for reachs)
         new._stricklers = StricklersList._db_load(
-            execute,
+            execute, data
-            data
         )
         data["stricklers"] = new._stricklers
 
         # Initial conditions
         new._sediment_layers = SedimentLayerList._db_load(
-            execute,
+            execute, data
-            data
         )
         data["sediment_layers_list"] = new._sediment_layers
 
         # Network
         new._nodes = RiverNode._db_load(
-            execute,
+            execute, data
-            data
         )
         data["nodes"] = new.nodes()
 
         new._edges = RiverReach._db_load(
-            execute,
+            execute, data
-            data
         )
         data["edges"] = new.edges()
 
         # Boundary Condition
         new._boundary_condition = BoundaryConditionList._db_load(
-            execute,
+            execute, data
-            data
         )
         # Lateral Contribution
         new._lateral_contribution = LateralContributionList._db_load(
-            execute,
+            execute, data
-            data
         )
 
         # Initial conditions
         new._initial_conditions = InitialConditionsDict._db_load(
-            execute,
+            execute, data
-            data
         )
 
         # Reservoir
         new._reservoir = ReservoirList._db_load(
-            execute,
+            execute, data
-            data
         )
 
         # Hydraulic Structures
         new._hydraulic_structures = HydraulicStructureList._db_load(
-            execute,
+            execute, data
-            data
         )
 
         # Parameters
         new._parameters = SolverParametersList._db_load(
-            execute,
+            execute, data
-            data
         )
 
+        # Additional Files
+        new._additional_files = AddFileList._db_load(
+            execute, data
+        )
+        new._rep_lines = REPLineList._db_load(execute, data)
+
         return new
 
     def _db_save(self, execute, data=None):
@@ -336,6 +338,8 @@ class River(Graph, SQLSubModel):
         objs.append(self._stricklers)
         objs.append(self._reservoir)
         objs.append(self._hydraulic_structures)
+        objs.append(self._additional_files)
+        objs.append(self._rep_lines)
 
         for solver in self._parameters:
             objs.append(self._parameters[solver])
@@ -372,6 +376,43 @@ class River(Graph, SQLSubModel):
         except Exception as e:
             logger_exception(e)
 
+    def init_default(self):
+        self.init_default_network()
+        self.init_default_sediment()
+        self.init_default_additional_files()
+
+    def init_default_network(self):
+        n1 = self.add_node(880.0, 950.0)
+        n2 = self.add_node(1120.0, 1020.0)
+
+        e = self.add_edge(n1, n2)
+
+    def init_default_sediment(self):
+        sediment = self._sediment_layers
+        default = sediment.new(0)
+        default_0 = default.new(0)
+
+        default.name = "default"
+        default.comment = "Default sediment layers"
+
+        default_0.name = "L0"
+        default_0.height = 1.0
+        default_0.d50 = 0.002
+        default_0.sigma = 1.0
+        default_0.critical_constraint = 0.047
+
+    def init_default_additional_files(self):
+        add_file = self._additional_files.new(0)
+        add_file.name = "Pamhyr2 stamp file"
+        add_file.path = "Pamhyr2.txt"
+        add_file.text = """This repository has been generated by Pamhyr2 \
+version "@version" !
+
+All hand made file modification could be erased by the next solver
+execution...
+
+Last export at: @date."""
+
     @property
     def boundary_condition(self):
         return self._boundary_condition
@@ -413,6 +454,14 @@ class River(Graph, SQLSubModel):
     def hydraulic_structures(self):
         return self._hydraulic_structures
 
+    @property
+    def additional_files(self):
+        return self._additional_files
+
+    @property
+    def rep_lines(self):
+        return self._rep_lines
+
     @property
     def parameters(self):
         return self._parameters

src/Model/Saved.py

@@ -1,5 +1,5 @@
 # Saved.py -- Pamhyr model status class
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -22,10 +22,19 @@ logger = logging.getLogger()
 
 
 class SavedStatus(object):
-    def __init__(self):
+    def __init__(self, version=0):
         super(SavedStatus, self).__init__()
+        self._version = version
         self._saved = True
 
+    @property
+    def version(self):
+        return self._version
+
+    @version.setter
+    def version(self, version):
+        self._version = version
+
     def is_saved(self):
         return self._saved
 
@@ -34,5 +43,11 @@ class SavedStatus(object):
         self._saved = True
 
     def modified(self):
-        # logger.debug("model status set as modified")
+        if self._saved:
+            self._version += 1
+
+        logger.debug(
+            "STATUS: Model status set as modified " +
+            f"at version {self._version}"
+        )
         self._saved = False

src/Model/SedimentLayer/SedimentLayer.py

@@ -1,5 +1,23 @@
+# SedimentLayer.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 # -*- coding: utf-8 -*-
 
+from functools import reduce
+
 from tools import trace, timer
 
 from Model.Tools.PamhyrDB import SQLSubModel
@@ -37,6 +55,9 @@ class Layer(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"Layer{self.id + 1}"
+
         return self._name
 
     @name.setter
@@ -204,6 +225,9 @@ class SedimentLayer(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"SL{self.id + 1}"
+
         return self._name
 
     @name.setter
@@ -340,3 +364,29 @@ class SedimentLayer(SQLSubModel):
             lst[index], lst[prev] = lst[prev], lst[index]
 
             self._status.modified()
+
+    def compute_height_from_bottom(self, bottom_elevation: list):
+        sl_height = self.height()
+
+        sl_height_by_profile = []
+        for i in range(len(sl_height)):
+            cur_profile = []
+            for _ in bottom_elevation:
+                cur_profile.append(sl_height[i])
+
+            sl_height_by_profile.append(cur_profile)
+
+        z_sl = reduce(
+            lambda acc, current_sl: acc + [
+                list(
+                    map(
+                        lambda cur_sl_h, prev_sl_h: prev_sl_h - cur_sl_h,
+                        current_sl, acc[-1]
+                    )
+                )
+            ],
+            sl_height_by_profile,
+            [bottom_elevation]
+        )
+
+        return z_sl

src/Model/SedimentLayer/SedimentLayerList.py

@@ -1,3 +1,19 @@
+# SedimentLayerList.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 # -*- coding: utf-8 -*-
 
 from tools import trace, timer

src/Model/Serializable.py

@@ -1,5 +1,5 @@
 # Serializable.py -- Pamhyr pickle abstract class
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/SolverParameters/SolverParametersList.py

@@ -1,5 +1,5 @@
 # SolverParametersList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Stricklers/Stricklers.py

@@ -1,5 +1,5 @@
 # Stricklers.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -120,6 +120,8 @@ class Stricklers(SQLSubModel):
 
     @property
     def name(self):
+        if self._name == "":
+            return f"K{self.id + 1}"
         return self._name
 
     @name.setter

src/Model/Stricklers/StricklersList.py

@@ -1,5 +1,5 @@
 # StricklersList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/Study.py

@@ -1,5 +1,5 @@
 # Study.py -- Pamhyr Study class
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -41,7 +41,7 @@ class Study(SQLModel):
 
     def __init__(self, filename=None, init_new=True):
         # Metadata
-        self._version = "0.0.7"
+        self._version = "0.0.11"
         self.creation_date = datetime.now()
         self.last_modification_date = datetime.now()
         self.last_save_date = datetime.now()
@@ -71,6 +71,8 @@ class Study(SQLModel):
         lst = [
             StudyNetworkReachChecker(),
             StudyGeometryChecker(),
+            StudyInitialConditionsChecker(),
+            StudyBoundaryConditionChecker(),
             # DummyOK(),
             # DummyWARNING(),
             # DummyERROR(),
@@ -103,10 +105,23 @@ class Study(SQLModel):
             except Exception as e:
                 logger.error(e)
 
+        is_new = False
         fname = fname + "." + str(self._old_save_id)
-        filename = os.path.join(fdir, "_PAMHYR_", "__old__", fname)
+        if os.path.exists(self.filename) and ".backup" not in self.filename:
-        shutil.copy(self.filename, filename)
+            filename = os.path.join(fdir, "_PAMHYR_", "__old__", fname)
-        self._old_save_id += 1
+            logger.debug(f"Backup previous version copy: {filename}")
+            shutil.copy(self.filename, filename)
+            self._old_save_id += 1
+            is_new = True
+
+        if ".backup" in self.filename:
+            is_new = True
+
+        if not os.path.exists(self.filename):
+            is_new = True
+
+        self._init_db_file(self.filename, is_new=is_new)
+        self.commit()
 
         # Save
         self.last_save_date = datetime.now()
@@ -128,6 +143,16 @@ class Study(SQLModel):
 
     @filename.setter
     def filename(self, filename):
+        if filename is None:
+            self._filename = None
+            self.status.modified()
+            return
+
+        if self._filename is not None and self._filename != "":
+            self._filename = str(filename)
+            self.status.modified()
+            return
+
         self._filename = str(filename)
         self._init_db_file(filename, is_new=True)
         self.status.modified()
@@ -187,7 +212,12 @@ class Study(SQLModel):
     def _create(self):
         # Info (metadata)
         self.execute(
-            "CREATE TABLE info(key TEXT NOT NULL UNIQUE, value TEXT NOT NULL)")
+            "INSERT INTO info VALUES ('study_release', '0')"
+        )
+
+        self.execute(
+            "CREATE TABLE info(key TEXT NOT NULL UNIQUE, value TEXT NOT NULL)"
+        )
         self.execute(
             "INSERT INTO info VALUES ('version', " +
             f"'{self._db_format(self._version)}')",
@@ -196,19 +226,20 @@ class Study(SQLModel):
         self.execute("INSERT INTO info VALUES ('name', '')")
         self.execute("INSERT INTO info VALUES ('description', '')")
         self.execute(
-            f"INSERT INTO info VALUES ('time_system', '{self._time_system}')")
+            f"INSERT INTO info VALUES ('time_system', '{self._time_system}')"
+        )
         self.execute(
-            f"INSERT INTO info VALUES ('date', " +
+            "INSERT INTO info VALUES ('date', " +
-            "'{self._date.timestamp()}')"
+            f"'{self._date.timestamp()}')"
         )
 
         self.execute(
-            f"INSERT INTO info VALUES ('creation_date', " +
+            "INSERT INTO info VALUES ('creation_date', " +
-            "'{self.creation_time.timestamp()}')"
+            f"'{self.creation_date.timestamp()}')"
         )
         self.execute(
-            f"INSERT INTO info VALUES ('last_save_date', " +
+            "INSERT INTO info VALUES ('last_save_date', " +
-            "'{self.last_save_time.timestamp()}')"
+            f"'{self.last_save_date.timestamp()}')"
         )
 
         self._create_submodel()
@@ -221,7 +252,13 @@ class Study(SQLModel):
         if version[0] == self._version:
             return True
 
-        logger.info("Update database")
+        logger.debug("Update database")
+
+        major, minor, release = version[0].split('.')
+        if major == "0" and minor == "0" and int(release) < 10:
+            self.execute(
+                "INSERT INTO info VALUES ('study_release', '0')"
+            )
 
         if self._update_submodel(version[0]):
             self.execute(
@@ -236,6 +273,11 @@ class Study(SQLModel):
     def _load(cls, filename):
         new = cls(init_new=False, filename=filename)
 
+        version = new.execute(
+            "SELECT value FROM info WHERE key='study_release'"
+        )
+        new.status.version = int(version[0])
+
         # TODO: Load metadata
         new.name = new.execute("SELECT value FROM info WHERE key='name'")[0]
         new.description = new.execute(
@@ -270,6 +312,11 @@ class Study(SQLModel):
     def _save(self, progress=None):
         progress = progress if progress is not None else lambda: None
 
+        self.execute(
+            "INSERT INTO info VALUES ('study_release', " +
+            f"'{self.status.version}')"
+        )
+
         self.execute(
             f"UPDATE info SET " +
             f"value='{self._db_format(self.name)}' WHERE key='name'"

src/Model/Tools/PamhyrDB.py

@@ -1,5 +1,5 @@
 # PamhyrDB.py -- Pamhyr abstract model database classes
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -23,7 +23,7 @@ import logging
 from pathlib import Path
 from functools import reduce
 
-from tools import SQL
+from SQL import SQL
 from Model.Except import NotImplementedMethodeError
 
 logger = logging.getLogger()
@@ -35,8 +35,10 @@ class SQLModel(SQL):
     _sub_classes = []
 
     def _init_db_file(self, db, is_new=True):
-        exists = Path(db).exists()
+        if self._db is not None:
+            self._db.close()
 
+        exists = Path(db).exists()
         if exists and is_new:
             os.remove(db)
 
@@ -68,6 +70,7 @@ class SQLModel(SQL):
         return True
 
     def _create(self):
+
         raise NotImplementedMethodeError(self, self._create)
 
     def _update_submodel(self, version):

src/Model/Tools/PamhyrDict.py

@@ -1,5 +1,5 @@
 # PamhyrDict.py -- Pamhyr abstract dict for model classes
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -56,7 +56,7 @@ class PamhyrModelDict(SQLSubModel):
     def __len__(self):
         return len(self._dict)
 
-    def is_defined(self, key):
+    def __contains__(self, key):
         return key in self._dict
 
     def set(self, key, new):

src/Model/Tools/PamhyrList.py

@@ -1,5 +1,5 @@
 # PamhyrList.py -- Pamhyr Abstract List object for the Model
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -62,16 +62,27 @@ class PamhyrModelList(SQLSubModel):
 
     @property
     def lst(self):
+        """Return the PamhyrList as a Python list
+
+        Return the PamhyrList as a Python list.  This list is the
+        current list used in the PamhyrList object.  **If you need to
+        modify it, please make a copy.**
+
+        Returns: The Python list
+        """
         return self._lst
 
     def __len__(self):
         return len(self.lst)
 
-    def get(self, row):
+    def index(self, el):
-        return self._lst[row]
+        return self._lst.index(el)
 
-    def set(self, row, new):
+    def get(self, index):
-        self._lst[row] = new
+        return self._lst[index]
+
+    def set(self, index, new):
+        self._lst[index] = new
         if self._status is not None:
             self._status.modified()
 
@@ -93,6 +104,14 @@ class PamhyrModelList(SQLSubModel):
             self._status.modified()
 
     def delete(self, lst):
+        """Delete a list of elements
+
+        Args:
+            lst: The list of elements
+
+        Returns:
+            Nothing
+        """
         for el in lst:
             self._lst.remove(el)
 
@@ -100,6 +119,14 @@ class PamhyrModelList(SQLSubModel):
             self._status.modified()
 
     def delete_i(self, indexes):
+        """Delete elements from list of indexes
+
+        Args:
+            indexes: The elements indexes
+
+        Returns:
+            Nothing
+        """
         lst = list(
             map(
                 lambda x: x[1],
@@ -175,16 +202,32 @@ class PamhyrModelListWithTab(SQLSubModel):
     ################
 
     def len(self, lst):
+        """Size of tab list
+
+        Args:
+            lst: The tab name
+
+        Returns:
+            The size of the tab list
+        """
         return len(self._tabs[lst])
 
     def get_tab(self, lst):
+        """Get tab list (copy) from name
+
+        Args:
+            lst: The tab name
+
+        Returns:
+            Nothing
+        """
         return self._tabs[lst].copy()
 
-    def get(self, lst, row):
+    def get(self, lst, index):
-        return self._tabs[lst][row]
+        return self._tabs[lst][index]
 
-    def set(self, lst, row, new):
+    def set(self, lst, index, new):
-        self._tabs[lst][row] = new
+        self._tabs[lst][index] = new
         self._status.modified()
 
     def new(self, lst, index):
@@ -200,15 +243,43 @@ class PamhyrModelListWithTab(SQLSubModel):
         raise NotImplementedMethodeError(self, self.new)
 
     def insert(self, lst, index, new):
+        """Insert element in tab
+
+        Args:
+            lst: The tab name
+            index: The index of new element
+            new: The new elements
+
+        Returns:
+            Nothing
+        """
         self._tabs[lst].insert(index, new)
         self._status.modified()
 
     def delete(self, lst, els):
+        """Delete elements from specific tab
+
+        Args:
+            lst: The tab name
+            els: The elements list
+
+        Returns:
+            Nothing
+        """
         for el in els:
             self._tabs[lst].remove(el)
         self._status.modified()
 
     def delete_i(self, lst, indexes):
+        """Delete elements from specific tab
+
+        Args:
+            lst: The tab name
+            indexes: The elements indexes
+
+        Returns:
+            Nothing
+        """
         els = list(
             map(
                 lambda x: x[1],

src/Model/__init__.py

@@ -1,5 +1,5 @@
 # __init__.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Model/test_Model.py

@@ -1,5 +1,5 @@
 # test_Model.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Modules.py

@@ -0,0 +1,164 @@
+# Modules.py -- Pamhyr
+# Copyright (C) 2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import logging
+
+from enum import Flag, auto
+
+logger = logging.getLogger()
+
+
+class IterableFlag(Flag):
+    def __iter__(self):
+        all = filter(
+            lambda v: v in self,
+            type(self).values()
+        )
+        return all
+
+    @classmethod
+    def values(cls):
+        raise Exception("Not implemented yet")
+
+
+class Modules(IterableFlag):
+    NONE = 0
+
+    # General
+    STUDY = auto()
+    CONFIG = auto()
+
+    # Modelling
+    NETWORK = auto()
+    GEOMETRY = auto()
+    BOUNDARY_CONDITION = auto()
+    LATERAL_CONTRIBUTION = auto()
+    FRICTION = auto()
+    INITIAL_CONDITION = auto()
+    HYDRAULIC_STRUCTURES = auto()
+    RESERVOIR = auto()
+    SEDIMENT_LAYER = auto()
+    ADDITIONAL_FILES = auto()
+
+    # Results
+    RESULTS = auto()
+
+    # Display
+    WINDOW_LIST = auto()
+
+    @classmethod
+    def values(cls):
+        return [
+            cls.STUDY, cls.CONFIG,
+            cls.NETWORK,
+            cls.GEOMETRY,
+            cls.BOUNDARY_CONDITION,
+            cls.LATERAL_CONTRIBUTION,
+            cls.FRICTION,
+            cls.INITIAL_CONDITION,
+            cls.HYDRAULIC_STRUCTURES,
+            cls.RESERVOIR,
+            cls.SEDIMENT_LAYER,
+            cls.ADDITIONAL_FILES,
+            cls.RESULTS,
+            cls.WINDOW_LIST,
+        ]
+
+    @classmethod
+    def all(cls):
+        return ~cls.NONE
+
+    @classmethod
+    def modelling(cls):
+        return (
+            cls.NETWORK
+            | cls.GEOMETRY
+            | cls.BOUNDARY_CONDITION
+            | cls.LATERAL_CONTRIBUTION
+            | cls.FRICTION
+            | cls.INITIAL_CONDITION
+            | cls.HYDRAULIC_STRUCTURES
+            | cls.RESERVOIR
+            | cls.SEDIMENT_LAYER
+        )
+
+    @classmethod
+    def modelling_list(cls):
+        return [
+            cls.NETWORK,
+            cls.GEOMETRY,
+            cls.BOUNDARY_CONDITION,
+            cls.LATERAL_CONTRIBUTION,
+            cls.FRICTION,
+            cls.INITIAL_CONDITION,
+            cls.HYDRAULIC_STRUCTURES,
+            cls.RESERVOIR,
+            cls.SEDIMENT_LAYER,
+        ]
+
+    @classmethod
+    def modelling_display_name(cls):
+        return {
+            cls.NETWORK: "Network",
+            cls.GEOMETRY: "Geometry",
+            cls.BOUNDARY_CONDITION: "Boundary condition",
+            cls.LATERAL_CONTRIBUTION: "Lateral contribution",
+            cls.FRICTION: "Friction",
+            cls.INITIAL_CONDITION: "Initial condition",
+            cls.HYDRAULIC_STRUCTURES: "Hydraulic structures",
+            cls.RESERVOIR: "Reservoir",
+            cls.SEDIMENT_LAYER: "Sediment layer",
+        }
+
+    def impact(self):
+        res = Modules(0)
+        for mod in self:
+            if mod in _impact:
+                for i in _impact[mod]:
+                    res |= i
+        return res
+
+    def impact_set(self):
+        res = []
+        for mod in self:
+            if mod in _impact:
+                res += _impact[mod]
+
+        return set(res)
+
+
+_impact = {
+    Modules.NETWORK: [
+        Modules.GEOMETRY, Modules.BOUNDARY_CONDITION,
+        Modules.LATERAL_CONTRIBUTION, Modules.FRICTION,
+        Modules.RESERVOIR, Modules.SEDIMENT_LAYER,
+    ],
+    Modules.GEOMETRY: [
+        Modules.LATERAL_CONTRIBUTION, Modules.FRICTION,
+        Modules.INITIAL_CONDITION, Modules.SEDIMENT_LAYER,
+    ],
+    Modules.BOUNDARY_CONDITION: [
+        Modules.SEDIMENT_LAYER
+    ],
+    Modules.LATERAL_CONTRIBUTION: [],
+    Modules.FRICTION: [],
+    Modules.INITIAL_CONDITION: [],
+    Modules.HYDRAULIC_STRUCTURES: [],
+    Modules.RESERVOIR: [],
+    Modules.SEDIMENT_LAYER: [],
+}

src/SQL.py

@@ -0,0 +1,133 @@
+# SQL.py -- Pamhyr
+# Copyright (C) 2023-2024  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import os
+import logging
+import sqlite3
+
+from pathlib import Path
+
+from tools import timer
+
+logger = logging.getLogger()
+
+
+class SQL(object):
+    def _init_db_file(self, db):
+        exists = Path(db).exists()
+
+        os.makedirs(
+            os.path.dirname(db),
+            exist_ok=True
+        )
+
+        self._db = sqlite3.connect(db)
+        self._cur = self._db.cursor()
+
+        if not exists:
+            self._create()      # Create db
+            self._save()        # Save
+        else:
+            self._update()      # Update db scheme if necessary
+            self._load()        # Load data
+
+    def __init__(self, filename=None):
+        self._db = None
+
+        if filename is not None:
+            self._init_db_file(filename)
+
+    def commit(self):
+        logger.debug("SQL - commit")
+        self._db.commit()
+
+    def _close(self):
+        self.commit()
+        self._db.close()
+
+    def _fetch_string(self, s):
+        return s.replace("&#39;", "'")
+
+    def _fetch_tuple(self, tup):
+        res = []
+        for v in tup:
+            if type(v) is str:
+                v = self._fetch_string(v)
+            res.append(v)
+
+        return res
+
+    def _fetch_list(self, lst):
+        res = []
+        for v in lst:
+            if type(v) is str:
+                v = self._fetch_string(v)
+            elif type(v) is tuple:
+                v = self._fetch_tuple(v)
+            res.append(v)
+
+        return res
+
+    def _fetch(self, res, one):
+        if one:
+            value = res.fetchone()
+        else:
+            value = res.fetchall()
+        res = value
+
+        if type(value) is list:
+            res = self._fetch_list(value)
+        elif type(value) is tuple:
+            res = self._fetch_tuple(value)
+
+        return res
+
+    def _db_format(self, value):
+        # Replace ''' by '&#39;' to preserve SQL injection
+        if type(value) is str:
+            value = value.replace("'", "&#39;")
+        return value
+
+    @timer
+    def execute(self, cmd, fetch_one=True, commit=False):
+        logger.debug(f"SQL - {cmd}")
+
+        value = None
+        try:
+            res = self._cur.execute(cmd)
+
+            if commit:
+                self._db.commit()
+
+            value = self._fetch(res, fetch_one)
+        except Exception as e:
+            logger_exception(e)
+        finally:
+            return value
+
+    def _create(self):
+        logger.warning("TODO: Create")
+
+    def _update(self):
+        logger.warning("TODO: Update")
+
+    def _save(self):
+        logger.warning("TODO: Save")
+
+    def _load(self):
+        logger.warning("TODO: LOAD")

src/Scripts/AScript.py

@@ -1,5 +1,5 @@
 # AScript.py -- Pamhyr abstract script class
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Scripts/Hello.py

@@ -1,5 +1,5 @@
 # Hello.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Scripts/ListSolver.py

@@ -1,5 +1,5 @@
 # ListSolver.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Scripts/MageMesh.py

@@ -1,5 +1,5 @@
 # MageMesh.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Scripts/P3DST.py

@@ -1,5 +1,5 @@
 # P3DST.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Scripts/Run.py

@@ -1,5 +1,5 @@
 # Run.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

src/Solver/ASolver.py

@@ -1,5 +1,5 @@
 # ASolver.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2024  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by